Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Job stats: job count --------------------- ------- all 1 combine_fastas 1 combine_filtered_gffs 1 combine_gffs 1 create_filtered_gffs 556 create_heatmap_csv 1 fastas 556 mirna_node_tmp_file 1 parse_output 556 prepare_genome 1 search_CM 556 total 2231 Select jobs to execute... [Fri Nov 3 10:21:17 2023] rule prepare_genome: input: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna output: data/genomes/Amil-MirMachine.fai, data/genomes/Amil-MirMachine.size jobid: 4 reason: Missing output files: data/genomes/Amil-MirMachine.size resources: tmpdir=/tmp [Fri Nov 3 10:21:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-927.PRE.CM output: analyses/output/Amil-MirMachine/Mir-927.PRE.result jobid: 998 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-927.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-927.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:17 2023] rule mirna_node_tmp_file: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/nodes_mirnas_corrected.tsv output: analyses/search/Amil-MirMachine.mirna_nodes.csv jobid: 1673 reason: Missing output files: analyses/search/Amil-MirMachine.mirna_nodes.csv wildcards: species=Amil-MirMachine resources: tmpdir=/tmp [Fri Nov 3 10:21:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2707.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2707.PRE.result jobid: 430 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2707.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2707.PRE threads: 15 resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:21:19 2023] Finished job 4. 1 of 2231 steps (0.0%) done Removing temporary output data/genomes/Amil-MirMachine.fai. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:19 2023] Finished job 1673. 2 of 2231 steps (0.1%) done [Fri Nov 3 10:21:26 2023] Finished job 430. 3 of 2231 steps (0.1%) done [Fri Nov 3 10:21:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-8160.PRE.CM output: analyses/output/Amil-MirMachine/Mir-8160.PRE.result jobid: 966 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8160.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-8160.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2707.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2707.PRE.gff, analyses/output/Amil-MirMachine/Mir-2707.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2707.PRE.unfiltered jobid: 429 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2707.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2707.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2707.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:27 2023] Finished job 998. 4 of 2231 steps (0.2%) done Select jobs to execute... [Fri Nov 3 10:21:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-927.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-927.PRE.gff, analyses/output/Amil-MirMachine/Mir-927.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-927.PRE.unfiltered jobid: 997 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-927.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-927.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-927.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-142.PRE.CM output: analyses/output/Amil-MirMachine/Mir-142.PRE.result jobid: 126 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-142.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-142.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:28 2023] Finished job 429. 5 of 2231 steps (0.2%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2707.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:21:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2707.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2707.PRE.filtered.gff jobid: 1329 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2707.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2707.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2707.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2707.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2707.PRE.filtered.fasta jobid: 1888 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2707.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2707.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2707.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:28 2023] Finished job 1888. 6 of 2231 steps (0.3%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:28 2023] Finished job 1329. 7 of 2231 steps (0.3%) done [Fri Nov 3 10:21:29 2023] Finished job 997. 8 of 2231 steps (0.4%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-927.PRE.ext.gff. [Fri Nov 3 10:21:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-927.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-927.PRE.filtered.fasta jobid: 2172 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-927.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-927.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-927.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-927.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-927.PRE.filtered.gff jobid: 1613 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-927.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-927.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-927.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:29 2023] Finished job 2172. 9 of 2231 steps (0.4%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:30 2023] Finished job 1613. 10 of 2231 steps (0.4%) done [Fri Nov 3 10:21:30 2023] Finished job 966. 11 of 2231 steps (0.5%) done [Fri Nov 3 10:21:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-8160.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-8160.PRE.gff, analyses/output/Amil-MirMachine/Mir-8160.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-8160.PRE.unfiltered jobid: 965 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8160.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-8160.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-8160.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4983.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4983.PRE.result jobid: 726 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4983.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4983.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:30 2023] Finished job 965. 12 of 2231 steps (1%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-8160.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:21:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-8160.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-8160.PRE.filtered.fasta jobid: 2156 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8160.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-8160.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-8160.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-8160.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-8160.PRE.filtered.gff jobid: 1597 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8160.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-8160.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-8160.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:30 2023] Finished job 2156. 13 of 2231 steps (1%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:31 2023] Finished job 1597. 14 of 2231 steps (1%) done [Fri Nov 3 10:21:33 2023] Finished job 126. 15 of 2231 steps (1%) done [Fri Nov 3 10:21:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-142.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-142.PRE.gff, analyses/output/Amil-MirMachine/Mir-142.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-142.PRE.unfiltered jobid: 125 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-142.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-142.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-142.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1788.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1788.PRE.result jobid: 186 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1788.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1788.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:34 2023] Finished job 125. 16 of 2231 steps (1%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-142.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:21:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-142.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-142.PRE.filtered.fasta jobid: 1736 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-142.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-142.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-142.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-142.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-142.PRE.filtered.gff jobid: 1177 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-142.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-142.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-142.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:34 2023] Finished job 1736. 17 of 2231 steps (1%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:34 2023] Finished job 1177. 18 of 2231 steps (1%) done [Fri Nov 3 10:21:41 2023] Finished job 186. 19 of 2231 steps (1%) done [Fri Nov 3 10:21:41 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1788.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1788.PRE.gff, analyses/output/Amil-MirMachine/Mir-1788.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1788.PRE.unfiltered jobid: 185 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1788.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1788.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1788.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:41 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-723.PRE.CM output: analyses/output/Amil-MirMachine/Mir-723.PRE.result jobid: 846 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-723.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-723.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:41 2023] Finished job 185. 20 of 2231 steps (1%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1788.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:21:41 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1788.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1788.PRE.filtered.gff jobid: 1207 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1788.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1788.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1788.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:41 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1788.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1788.PRE.filtered.fasta jobid: 1766 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1788.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1788.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1788.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:41 2023] Finished job 1766. 21 of 2231 steps (1%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:42 2023] Finished job 1207. 22 of 2231 steps (1%) done [Fri Nov 3 10:21:48 2023] Finished job 726. 23 of 2231 steps (1%) done [Fri Nov 3 10:21:48 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4983.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4983.PRE.gff, analyses/output/Amil-MirMachine/Mir-4983.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4983.PRE.unfiltered jobid: 725 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4983.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4983.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4983.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:48 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Iab-4.PRE.CM output: analyses/output/Amil-MirMachine/Iab-4.PRE.result jobid: 6 reason: Missing output files: analyses/output/Amil-MirMachine/Iab-4.PRE.result wildcards: species=Amil-MirMachine, mirna=Iab-4.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:48 2023] Finished job 725. 24 of 2231 steps (1%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4983.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:21:48 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4983.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4983.PRE.filtered.fasta jobid: 2036 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4983.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4983.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4983.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:48 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4983.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4983.PRE.filtered.gff jobid: 1477 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4983.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4983.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4983.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:48 2023] Finished job 2036. 25 of 2231 steps (1%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:49 2023] Finished job 1477. 26 of 2231 steps (1%) done [Fri Nov 3 10:21:56 2023] Finished job 6. 27 of 2231 steps (1%) done [Fri Nov 3 10:21:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Iab-4.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Iab-4.PRE.gff, analyses/output/Amil-MirMachine/Iab-4.PRE.ext.gff, analyses/output/Amil-MirMachine/Iab-4.PRE.unfiltered jobid: 5 reason: Missing output files: analyses/output/Amil-MirMachine/Iab-4.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Iab-4.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Iab-4.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-450.PRE.CM output: analyses/output/Amil-MirMachine/Mir-450.PRE.result jobid: 606 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-450.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-450.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] Finished job 5. 28 of 2231 steps (1%) done Removing temporary output analyses/output/Amil-MirMachine/Iab-4.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:21:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Iab-4.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Iab-4.PRE.filtered.fasta jobid: 1676 reason: Missing output files: analyses/output/Amil-MirMachine/Iab-4.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Iab-4.PRE.gff wildcards: species=Amil-MirMachine, mirna=Iab-4.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Iab-4.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Iab-4.PRE.filtered.gff jobid: 1117 reason: Missing output files: analyses/output/Amil-MirMachine/Iab-4.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Iab-4.PRE.gff wildcards: species=Amil-MirMachine, mirna=Iab-4.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] Finished job 846. 29 of 2231 steps (1%) done Select jobs to execute... [Fri Nov 3 10:21:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-723.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-723.PRE.gff, analyses/output/Amil-MirMachine/Mir-723.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-723.PRE.unfiltered jobid: 845 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-723.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-723.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-723.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7368.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7368.PRE.result jobid: 906 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7368.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7368.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] Finished job 1676. 30 of 2231 steps (1%) done Select jobs to execute... [Fri Nov 3 10:21:56 2023] Finished job 845. 31 of 2231 steps (1%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-723.PRE.ext.gff. [Fri Nov 3 10:21:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-723.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-723.PRE.filtered.fasta jobid: 2096 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-723.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-723.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-723.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-723.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-723.PRE.filtered.gff jobid: 1537 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-723.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-723.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-723.PRE resources: tmpdir=/tmp [Fri Nov 3 10:21:56 2023] Finished job 2096. 32 of 2231 steps (1%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:56 2023] Finished job 1117. 33 of 2231 steps (1%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:21:57 2023] Finished job 1537. 34 of 2231 steps (2%) done [Fri Nov 3 10:22:00 2023] Finished job 906. 35 of 2231 steps (2%) done [Fri Nov 3 10:22:00 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7368.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7368.PRE.gff, analyses/output/Amil-MirMachine/Mir-7368.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7368.PRE.unfiltered jobid: 905 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7368.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7368.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7368.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:00 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-204.PRE.CM output: analyses/output/Amil-MirMachine/Mir-204.PRE.result jobid: 306 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-204.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-204.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:00 2023] Finished job 905. 36 of 2231 steps (2%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7368.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:00 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7368.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7368.PRE.filtered.gff jobid: 1567 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7368.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7368.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7368.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:00 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7368.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7368.PRE.filtered.fasta jobid: 2126 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7368.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7368.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7368.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:00 2023] Finished job 2126. 37 of 2231 steps (2%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:01 2023] Finished job 1567. 38 of 2231 steps (2%) done [Fri Nov 3 10:22:03 2023] Finished job 606. 39 of 2231 steps (2%) done [Fri Nov 3 10:22:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-450.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-450.PRE.gff, analyses/output/Amil-MirMachine/Mir-450.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-450.PRE.unfiltered jobid: 605 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-450.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-450.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-450.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1251.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1251.PRE.result jobid: 66 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1251.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1251.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:03 2023] Finished job 605. 40 of 2231 steps (2%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-450.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-450.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-450.PRE.filtered.fasta jobid: 1976 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-450.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-450.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-450.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-450.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-450.PRE.filtered.gff jobid: 1417 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-450.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-450.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-450.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:03 2023] Finished job 1976. 41 of 2231 steps (2%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:03 2023] Finished job 1417. 42 of 2231 steps (2%) done [Fri Nov 3 10:22:06 2023] Finished job 306. 43 of 2231 steps (2%) done [Fri Nov 3 10:22:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7363.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7363.PRE.result jobid: 904 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7363.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7363.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-204.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-204.PRE.gff, analyses/output/Amil-MirMachine/Mir-204.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-204.PRE.unfiltered jobid: 305 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-204.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-204.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-204.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:06 2023] Finished job 305. 44 of 2231 steps (2%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-204.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-204.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-204.PRE.filtered.fasta jobid: 1826 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-204.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-204.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-204.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-204.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-204.PRE.filtered.gff jobid: 1267 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-204.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-204.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-204.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:06 2023] Finished job 1826. 45 of 2231 steps (2%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:06 2023] Finished job 1267. 46 of 2231 steps (2%) done [Fri Nov 3 10:22:08 2023] Finished job 66. 47 of 2231 steps (2%) done [Fri Nov 3 10:22:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1781.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1781.PRE.result jobid: 184 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1781.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1781.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1251.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1251.PRE.gff, analyses/output/Amil-MirMachine/Mir-1251.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1251.PRE.unfiltered jobid: 65 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1251.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1251.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1251.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:08 2023] Finished job 65. 48 of 2231 steps (2%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1251.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1251.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1251.PRE.filtered.fasta jobid: 1706 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1251.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1251.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1251.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1251.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1251.PRE.filtered.gff jobid: 1147 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1251.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1251.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1251.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:08 2023] Finished job 1706. 49 of 2231 steps (2%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:09 2023] Finished job 1147. 50 of 2231 steps (2%) done [Fri Nov 3 10:22:10 2023] Finished job 904. 51 of 2231 steps (2%) done [Fri Nov 3 10:22:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-140.PRE.CM output: analyses/output/Amil-MirMachine/Mir-140.PRE.result jobid: 122 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-140.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-140.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7363.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7363.PRE.gff, analyses/output/Amil-MirMachine/Mir-7363.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7363.PRE.unfiltered jobid: 903 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7363.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7363.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7363.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:10 2023] Finished job 903. 52 of 2231 steps (2%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7363.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7363.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7363.PRE.filtered.gff jobid: 1566 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7363.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7363.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7363.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7363.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7363.PRE.filtered.fasta jobid: 2125 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7363.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7363.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7363.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:10 2023] Finished job 2125. 53 of 2231 steps (2%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:10 2023] Finished job 1566. 54 of 2231 steps (2%) done [Fri Nov 3 10:22:15 2023] Finished job 122. 55 of 2231 steps (2%) done [Fri Nov 3 10:22:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-140.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-140.PRE.gff, analyses/output/Amil-MirMachine/Mir-140.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-140.PRE.unfiltered jobid: 121 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-140.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-140.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-140.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1729.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1729.PRE.result jobid: 182 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1729.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1729.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:15 2023] Finished job 121. 56 of 2231 steps (3%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-140.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-140.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-140.PRE.filtered.gff jobid: 1175 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-140.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-140.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-140.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-140.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-140.PRE.filtered.fasta jobid: 1734 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-140.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-140.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-140.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:15 2023] Finished job 1734. 57 of 2231 steps (3%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:15 2023] Finished job 1175. 58 of 2231 steps (3%) done [Fri Nov 3 10:22:16 2023] Finished job 184. 59 of 2231 steps (3%) done [Fri Nov 3 10:22:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7180.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7180.PRE.result jobid: 842 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7180.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7180.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1781.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1781.PRE.gff, analyses/output/Amil-MirMachine/Mir-1781.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1781.PRE.unfiltered jobid: 183 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1781.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1781.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1781.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:16 2023] Finished job 183. 60 of 2231 steps (3%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1781.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1781.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1781.PRE.filtered.gff jobid: 1206 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1781.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1781.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1781.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1781.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1781.PRE.filtered.fasta jobid: 1765 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1781.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1781.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1781.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:16 2023] Finished job 1765. 61 of 2231 steps (3%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:17 2023] Finished job 1206. 62 of 2231 steps (3%) done [Fri Nov 3 10:22:18 2023] Finished job 182. 63 of 2231 steps (3%) done [Fri Nov 3 10:22:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1729.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1729.PRE.gff, analyses/output/Amil-MirMachine/Mir-1729.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1729.PRE.unfiltered jobid: 181 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1729.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1729.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1729.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-734.PRE.CM output: analyses/output/Amil-MirMachine/Mir-734.PRE.result jobid: 902 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-734.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-734.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:18 2023] Finished job 181. 64 of 2231 steps (3%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1729.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:18 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1729.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1729.PRE.filtered.gff jobid: 1205 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1729.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1729.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1729.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:18 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1729.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1729.PRE.filtered.fasta jobid: 1764 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1729.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1729.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1729.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:18 2023] Finished job 1764. 65 of 2231 steps (3%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:19 2023] Finished job 1205. 66 of 2231 steps (3%) done [Fri Nov 3 10:22:20 2023] Finished job 842. 67 of 2231 steps (3%) done [Fri Nov 3 10:22:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7180.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7180.PRE.gff, analyses/output/Amil-MirMachine/Mir-7180.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7180.PRE.unfiltered jobid: 841 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7180.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7180.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7180.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-791.PRE.CM output: analyses/output/Amil-MirMachine/Mir-791.PRE.result jobid: 962 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-791.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-791.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:20 2023] Finished job 841. 68 of 2231 steps (3%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7180.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7180.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7180.PRE.filtered.gff jobid: 1535 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7180.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7180.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7180.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7180.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7180.PRE.filtered.fasta jobid: 2094 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7180.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7180.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7180.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:20 2023] Finished job 2094. 69 of 2231 steps (3%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:21 2023] Finished job 1535. 70 of 2231 steps (3%) done [Fri Nov 3 10:22:26 2023] Finished job 902. 71 of 2231 steps (3%) done [Fri Nov 3 10:22:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-734.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-734.PRE.gff, analyses/output/Amil-MirMachine/Mir-734.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-734.PRE.unfiltered jobid: 901 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-734.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-734.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-734.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4969.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4969.PRE.result jobid: 722 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4969.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4969.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:26 2023] Finished job 901. 72 of 2231 steps (3%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-734.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-734.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-734.PRE.filtered.gff jobid: 1565 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-734.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-734.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-734.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-734.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-734.PRE.filtered.fasta jobid: 2124 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-734.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-734.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-734.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:26 2023] Finished job 2124. 73 of 2231 steps (3%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:27 2023] Finished job 1565. 74 of 2231 steps (3%) done [Fri Nov 3 10:22:28 2023] Finished job 962. 75 of 2231 steps (3%) done [Fri Nov 3 10:22:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-791.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-791.PRE.gff, analyses/output/Amil-MirMachine/Mir-791.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-791.PRE.unfiltered jobid: 961 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-791.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-791.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-791.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-223.PRE.CM output: analyses/output/Amil-MirMachine/Mir-223.PRE.result jobid: 362 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-223.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-223.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:28 2023] Finished job 961. 76 of 2231 steps (3%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-791.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-791.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-791.PRE.filtered.gff jobid: 1595 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-791.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-791.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-791.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-791.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-791.PRE.filtered.fasta jobid: 2154 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-791.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-791.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-791.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:28 2023] Finished job 2154. 77 of 2231 steps (3%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:28 2023] Finished job 1595. 78 of 2231 steps (3%) done [Fri Nov 3 10:22:31 2023] Finished job 722. 79 of 2231 steps (4%) done [Fri Nov 3 10:22:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4969.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4969.PRE.gff, analyses/output/Amil-MirMachine/Mir-4969.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4969.PRE.unfiltered jobid: 721 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4969.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4969.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4969.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Bantam.PRE.CM output: analyses/output/Amil-MirMachine/Bantam.PRE.result jobid: 3 reason: Missing output files: analyses/output/Amil-MirMachine/Bantam.PRE.result wildcards: species=Amil-MirMachine, mirna=Bantam.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:31 2023] Finished job 721. 80 of 2231 steps (4%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4969.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4969.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4969.PRE.filtered.gff jobid: 1475 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4969.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4969.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4969.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4969.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4969.PRE.filtered.fasta jobid: 2034 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4969.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4969.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4969.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:31 2023] Finished job 2034. 81 of 2231 steps (4%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:32 2023] Finished job 1475. 82 of 2231 steps (4%) done [Fri Nov 3 10:22:38 2023] Finished job 362. 83 of 2231 steps (4%) done [Fri Nov 3 10:22:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3075.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3075.PRE.result jobid: 486 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3075.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3075.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-223.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-223.PRE.gff, analyses/output/Amil-MirMachine/Mir-223.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-223.PRE.unfiltered jobid: 361 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-223.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-223.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-223.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:38 2023] Finished job 361. 84 of 2231 steps (4%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-223.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-223.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-223.PRE.filtered.gff jobid: 1295 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-223.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-223.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-223.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-223.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-223.PRE.filtered.fasta jobid: 1854 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-223.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-223.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-223.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:38 2023] Finished job 1854. 85 of 2231 steps (4%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:38 2023] Finished job 1295. 86 of 2231 steps (4%) done [Fri Nov 3 10:22:42 2023] Finished job 3. 87 of 2231 steps (4%) done [Fri Nov 3 10:22:42 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-345.PRE.CM output: analyses/output/Amil-MirMachine/Mir-345.PRE.result jobid: 546 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-345.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-345.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:42 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Bantam.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Bantam.PRE.gff, analyses/output/Amil-MirMachine/Bantam.PRE.ext.gff, analyses/output/Amil-MirMachine/Bantam.PRE.unfiltered jobid: 2 reason: Missing output files: analyses/output/Amil-MirMachine/Bantam.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Bantam.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Bantam.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:42 2023] Finished job 2. 88 of 2231 steps (4%) done Removing temporary output analyses/output/Amil-MirMachine/Bantam.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Bantam.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Bantam.PRE.filtered.fasta jobid: 1675 reason: Missing output files: analyses/output/Amil-MirMachine/Bantam.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Bantam.PRE.gff wildcards: species=Amil-MirMachine, mirna=Bantam.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Bantam.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Bantam.PRE.filtered.gff jobid: 1116 reason: Missing output files: analyses/output/Amil-MirMachine/Bantam.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Bantam.PRE.gff wildcards: species=Amil-MirMachine, mirna=Bantam.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:42 2023] Finished job 1675. 89 of 2231 steps (4%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:42 2023] Finished job 1116. 90 of 2231 steps (4%) done [Fri Nov 3 10:22:42 2023] Finished job 486. 91 of 2231 steps (4%) done [Fri Nov 3 10:22:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-8.PRE.CM output: analyses/output/Amil-MirMachine/Mir-8.PRE.result jobid: 964 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-8.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3075.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3075.PRE.gff, analyses/output/Amil-MirMachine/Mir-3075.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3075.PRE.unfiltered jobid: 485 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3075.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3075.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3075.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:43 2023] Finished job 485. 92 of 2231 steps (4%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3075.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3075.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3075.PRE.filtered.fasta jobid: 1916 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3075.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3075.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3075.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3075.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3075.PRE.filtered.gff jobid: 1357 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3075.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3075.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3075.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:43 2023] Finished job 1916. 93 of 2231 steps (4%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:43 2023] Finished job 1357. 94 of 2231 steps (4%) done [Fri Nov 3 10:22:45 2023] Finished job 546. 95 of 2231 steps (4%) done [Fri Nov 3 10:22:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-498.PRE.CM output: analyses/output/Amil-MirMachine/Mir-498.PRE.result jobid: 724 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-498.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-498.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-345.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-345.PRE.gff, analyses/output/Amil-MirMachine/Mir-345.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-345.PRE.unfiltered jobid: 545 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-345.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-345.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-345.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:45 2023] Finished job 545. 96 of 2231 steps (4%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-345.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-345.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-345.PRE.filtered.fasta jobid: 1946 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-345.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-345.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-345.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-345.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-345.PRE.filtered.gff jobid: 1387 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-345.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-345.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-345.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:45 2023] Finished job 1946. 97 of 2231 steps (4%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:46 2023] Finished job 1387. 98 of 2231 steps (4%) done [Fri Nov 3 10:22:47 2023] Finished job 964. 99 of 2231 steps (4%) done [Fri Nov 3 10:22:48 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2030.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2030.PRE.result jobid: 304 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2030.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2030.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:48 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-8.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-8.PRE.gff, analyses/output/Amil-MirMachine/Mir-8.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-8.PRE.unfiltered jobid: 963 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-8.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-8.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:48 2023] Finished job 963. 100 of 2231 steps (4%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-8.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:48 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-8.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-8.PRE.filtered.fasta jobid: 2155 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-8.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-8.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:48 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-8.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-8.PRE.filtered.gff jobid: 1596 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-8.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-8.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-8.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:48 2023] Finished job 2155. 101 of 2231 steps (5%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:48 2023] Finished job 1596. 102 of 2231 steps (5%) done [Fri Nov 3 10:22:49 2023] Finished job 724. 103 of 2231 steps (5%) done [Fri Nov 3 10:22:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1249.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1249.PRE.result jobid: 64 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1249.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1249.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-498.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-498.PRE.gff, analyses/output/Amil-MirMachine/Mir-498.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-498.PRE.unfiltered jobid: 723 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-498.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-498.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-498.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:49 2023] Finished job 723. 104 of 2231 steps (5%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-498.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-498.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-498.PRE.filtered.fasta jobid: 2035 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-498.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-498.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-498.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-498.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-498.PRE.filtered.gff jobid: 1476 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-498.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-498.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-498.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:49 2023] Finished job 2035. 105 of 2231 steps (5%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:50 2023] Finished job 1476. 106 of 2231 steps (5%) done [Fri Nov 3 10:22:54 2023] Finished job 64. 107 of 2231 steps (5%) done [Fri Nov 3 10:22:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1247.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1247.PRE.result jobid: 62 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1247.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1247.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1249.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1249.PRE.gff, analyses/output/Amil-MirMachine/Mir-1249.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1249.PRE.unfiltered jobid: 63 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1249.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1249.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1249.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] Finished job 63. 108 of 2231 steps (5%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1249.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1249.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1249.PRE.filtered.gff jobid: 1146 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1249.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1249.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1249.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1249.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1249.PRE.filtered.fasta jobid: 1705 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1249.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1249.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1249.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] Finished job 1705. 109 of 2231 steps (5%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:55 2023] Finished job 1146. 110 of 2231 steps (5%) done [Fri Nov 3 10:22:55 2023] Finished job 304. 111 of 2231 steps (5%) done [Fri Nov 3 10:22:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-224.PRE.CM output: analyses/output/Amil-MirMachine/Mir-224.PRE.result jobid: 364 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-224.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-224.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2030.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2030.PRE.gff, analyses/output/Amil-MirMachine/Mir-2030.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2030.PRE.unfiltered jobid: 303 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2030.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2030.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2030.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] Finished job 303. 112 of 2231 steps (5%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2030.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2030.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2030.PRE.filtered.gff jobid: 1266 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2030.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2030.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2030.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2030.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2030.PRE.filtered.fasta jobid: 1825 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2030.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2030.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2030.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:55 2023] Finished job 1825. 113 of 2231 steps (5%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:56 2023] Finished job 1266. 114 of 2231 steps (5%) done [Fri Nov 3 10:22:58 2023] Finished job 62. 115 of 2231 steps (5%) done [Fri Nov 3 10:22:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-448.PRE.CM output: analyses/output/Amil-MirMachine/Mir-448.PRE.result jobid: 604 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-448.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-448.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:22:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1247.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1247.PRE.gff, analyses/output/Amil-MirMachine/Mir-1247.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1247.PRE.unfiltered jobid: 61 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1247.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1247.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1247.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:58 2023] Finished job 61. 116 of 2231 steps (5%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1247.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:22:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1247.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1247.PRE.filtered.gff jobid: 1145 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1247.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1247.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1247.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1247.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1247.PRE.filtered.fasta jobid: 1704 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1247.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1247.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1247.PRE resources: tmpdir=/tmp [Fri Nov 3 10:22:58 2023] Finished job 1704. 117 of 2231 steps (5%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:22:58 2023] Finished job 1145. 118 of 2231 steps (5%) done [Fri Nov 3 10:23:01 2023] Finished job 364. 119 of 2231 steps (5%) done [Fri Nov 3 10:23:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-722.PRE.CM output: analyses/output/Amil-MirMachine/Mir-722.PRE.result jobid: 844 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-722.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-722.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-224.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-224.PRE.gff, analyses/output/Amil-MirMachine/Mir-224.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-224.PRE.unfiltered jobid: 363 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-224.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-224.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-224.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:01 2023] Finished job 363. 120 of 2231 steps (5%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-224.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-224.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-224.PRE.filtered.fasta jobid: 1855 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-224.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-224.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-224.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-224.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-224.PRE.filtered.gff jobid: 1296 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-224.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-224.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-224.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:01 2023] Finished job 1855. 121 of 2231 steps (5%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:02 2023] Finished job 1296. 122 of 2231 steps (5%) done [Fri Nov 3 10:23:04 2023] Finished job 604. 123 of 2231 steps (6%) done [Fri Nov 3 10:23:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-433.PRE.CM output: analyses/output/Amil-MirMachine/Mir-433.PRE.result jobid: 602 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-433.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-433.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-448.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-448.PRE.gff, analyses/output/Amil-MirMachine/Mir-448.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-448.PRE.unfiltered jobid: 603 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-448.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-448.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-448.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:04 2023] Finished job 603. 124 of 2231 steps (6%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-448.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-448.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-448.PRE.filtered.fasta jobid: 1975 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-448.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-448.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-448.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-448.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-448.PRE.filtered.gff jobid: 1416 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-448.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-448.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-448.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:04 2023] Finished job 1975. 125 of 2231 steps (6%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:04 2023] Finished job 1416. 126 of 2231 steps (6%) done [Fri Nov 3 10:23:08 2023] Finished job 602. 127 of 2231 steps (6%) done [Fri Nov 3 10:23:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1416.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1416.PRE.result jobid: 124 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1416.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1416.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-433.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-433.PRE.gff, analyses/output/Amil-MirMachine/Mir-433.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-433.PRE.unfiltered jobid: 601 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-433.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-433.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-433.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:08 2023] Finished job 601. 128 of 2231 steps (6%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-433.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-433.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-433.PRE.filtered.gff jobid: 1415 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-433.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-433.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-433.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-433.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-433.PRE.filtered.fasta jobid: 1974 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-433.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-433.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-433.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:08 2023] Finished job 1974. 129 of 2231 steps (6%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:08 2023] Finished job 1415. 130 of 2231 steps (6%) done [Fri Nov 3 10:23:16 2023] Finished job 124. 131 of 2231 steps (6%) done [Fri Nov 3 10:23:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2279.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2279.PRE.result jobid: 366 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2279.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2279.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1416.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1416.PRE.gff, analyses/output/Amil-MirMachine/Mir-1416.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1416.PRE.unfiltered jobid: 123 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1416.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1416.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1416.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:16 2023] Finished job 123. 132 of 2231 steps (6%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1416.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1416.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1416.PRE.filtered.fasta jobid: 1735 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1416.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1416.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1416.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1416.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1416.PRE.filtered.gff jobid: 1176 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1416.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1416.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1416.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:16 2023] Finished job 1735. 133 of 2231 steps (6%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:17 2023] Finished job 1176. 134 of 2231 steps (6%) done [Fri Nov 3 10:23:19 2023] Finished job 844. 135 of 2231 steps (6%) done [Fri Nov 3 10:23:19 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Let-7.PRE.CM output: analyses/output/Amil-MirMachine/Let-7.PRE.result jobid: 8 reason: Missing output files: analyses/output/Amil-MirMachine/Let-7.PRE.result wildcards: species=Amil-MirMachine, mirna=Let-7.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:19 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-722.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-722.PRE.gff, analyses/output/Amil-MirMachine/Mir-722.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-722.PRE.unfiltered jobid: 843 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-722.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-722.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-722.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:20 2023] Finished job 843. 136 of 2231 steps (6%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-722.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-722.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-722.PRE.filtered.fasta jobid: 2095 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-722.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-722.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-722.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-722.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-722.PRE.filtered.gff jobid: 1536 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-722.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-722.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-722.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:20 2023] Finished job 2095. 137 of 2231 steps (6%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:20 2023] Finished job 1536. 138 of 2231 steps (6%) done [Fri Nov 3 10:23:23 2023] Finished job 366. 139 of 2231 steps (6%) done [Fri Nov 3 10:23:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2279.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2279.PRE.gff, analyses/output/Amil-MirMachine/Mir-2279.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2279.PRE.unfiltered jobid: 365 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2279.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2279.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2279.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-203.PRE.CM output: analyses/output/Amil-MirMachine/Mir-203.PRE.result jobid: 302 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-203.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-203.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:24 2023] Finished job 365. 140 of 2231 steps (6%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2279.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2279.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2279.PRE.filtered.fasta jobid: 1856 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2279.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2279.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2279.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2279.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2279.PRE.filtered.gff jobid: 1297 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2279.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2279.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2279.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:24 2023] Finished job 1856. 141 of 2231 steps (6%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:24 2023] Finished job 1297. 142 of 2231 steps (6%) done [Fri Nov 3 10:23:26 2023] Finished job 8. 143 of 2231 steps (6%) done [Fri Nov 3 10:23:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Let-7.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Let-7.PRE.gff, analyses/output/Amil-MirMachine/Let-7.PRE.ext.gff, analyses/output/Amil-MirMachine/Let-7.PRE.unfiltered jobid: 7 reason: Missing output files: analyses/output/Amil-MirMachine/Let-7.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Let-7.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Let-7.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-85.PRE.CM output: analyses/output/Amil-MirMachine/Mir-85.PRE.result jobid: 968 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-85.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-85.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:26 2023] Finished job 7. 144 of 2231 steps (6%) done Removing temporary output analyses/output/Amil-MirMachine/Let-7.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Let-7.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Let-7.PRE.filtered.gff jobid: 1118 reason: Missing output files: analyses/output/Amil-MirMachine/Let-7.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Let-7.PRE.gff wildcards: species=Amil-MirMachine, mirna=Let-7.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Let-7.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Let-7.PRE.filtered.fasta jobid: 1677 reason: Missing output files: analyses/output/Amil-MirMachine/Let-7.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Let-7.PRE.gff wildcards: species=Amil-MirMachine, mirna=Let-7.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:26 2023] Finished job 1677. 145 of 2231 steps (6%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:26 2023] Finished job 1118. 146 of 2231 steps (7%) done [Fri Nov 3 10:23:38 2023] Finished job 302. 147 of 2231 steps (7%) done [Fri Nov 3 10:23:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-221.PRE.CM output: analyses/output/Amil-MirMachine/Mir-221.PRE.result jobid: 360 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-221.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-221.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-203.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-203.PRE.gff, analyses/output/Amil-MirMachine/Mir-203.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-203.PRE.unfiltered jobid: 301 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-203.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-203.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-203.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:38 2023] Finished job 301. 148 of 2231 steps (7%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-203.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-203.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-203.PRE.filtered.gff jobid: 1265 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-203.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-203.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-203.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-203.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-203.PRE.filtered.fasta jobid: 1824 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-203.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-203.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-203.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:38 2023] Finished job 1824. 149 of 2231 steps (7%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:39 2023] Finished job 968. 150 of 2231 steps (7%) done [Fri Nov 3 10:23:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-85.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-85.PRE.gff, analyses/output/Amil-MirMachine/Mir-85.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-85.PRE.unfiltered jobid: 967 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-85.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-85.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-85.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-205.PRE.CM output: analyses/output/Amil-MirMachine/Mir-205.PRE.result jobid: 308 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-205.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-205.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:39 2023] Finished job 1265. 151 of 2231 steps (7%) done Select jobs to execute... [Fri Nov 3 10:23:39 2023] Finished job 967. 152 of 2231 steps (7%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-85.PRE.ext.gff. [Fri Nov 3 10:23:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-85.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-85.PRE.filtered.gff jobid: 1598 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-85.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-85.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-85.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-85.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-85.PRE.filtered.fasta jobid: 2157 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-85.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-85.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-85.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:39 2023] Finished job 2157. 153 of 2231 steps (7%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:39 2023] Finished job 1598. 154 of 2231 steps (7%) done [Fri Nov 3 10:23:44 2023] Finished job 360. 155 of 2231 steps (7%) done [Fri Nov 3 10:23:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-451.PRE.CM output: analyses/output/Amil-MirMachine/Mir-451.PRE.result jobid: 608 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-451.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-451.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-221.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-221.PRE.gff, analyses/output/Amil-MirMachine/Mir-221.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-221.PRE.unfiltered jobid: 359 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-221.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-221.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-221.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:44 2023] Finished job 359. 156 of 2231 steps (7%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-221.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-221.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-221.PRE.filtered.gff jobid: 1294 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-221.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-221.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-221.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-221.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-221.PRE.filtered.fasta jobid: 1853 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-221.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-221.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-221.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:44 2023] Finished job 1853. 157 of 2231 steps (7%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:45 2023] Finished job 1294. 158 of 2231 steps (7%) done [Fri Nov 3 10:23:46 2023] Finished job 308. 159 of 2231 steps (7%) done [Fri Nov 3 10:23:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-205.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-205.PRE.gff, analyses/output/Amil-MirMachine/Mir-205.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-205.PRE.unfiltered jobid: 307 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-205.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-205.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-205.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12404.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12404.PRE.result jobid: 60 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12404.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12404.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:46 2023] Finished job 307. 160 of 2231 steps (7%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-205.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-205.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-205.PRE.filtered.gff jobid: 1268 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-205.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-205.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-205.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-205.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-205.PRE.filtered.fasta jobid: 1827 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-205.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-205.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-205.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:46 2023] Finished job 1827. 161 of 2231 steps (7%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:46 2023] Finished job 1268. 162 of 2231 steps (7%) done [Fri Nov 3 10:23:49 2023] Finished job 608. 163 of 2231 steps (7%) done [Fri Nov 3 10:23:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-451.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-451.PRE.gff, analyses/output/Amil-MirMachine/Mir-451.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-451.PRE.unfiltered jobid: 607 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-451.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-451.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-451.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-499.PRE.CM output: analyses/output/Amil-MirMachine/Mir-499.PRE.result jobid: 728 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-499.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-499.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:49 2023] Finished job 607. 164 of 2231 steps (7%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-451.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-451.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-451.PRE.filtered.gff jobid: 1418 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-451.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-451.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-451.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-451.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-451.PRE.filtered.fasta jobid: 1977 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-451.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-451.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-451.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:49 2023] Finished job 1977. 165 of 2231 steps (7%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:50 2023] Finished job 1418. 166 of 2231 steps (7%) done [Fri Nov 3 10:23:50 2023] Finished job 60. 167 of 2231 steps (7%) done [Fri Nov 3 10:23:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-724.PRE.CM output: analyses/output/Amil-MirMachine/Mir-724.PRE.result jobid: 848 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-724.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-724.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12404.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12404.PRE.gff, analyses/output/Amil-MirMachine/Mir-12404.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12404.PRE.unfiltered jobid: 59 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12404.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12404.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12404.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:51 2023] Finished job 59. 168 of 2231 steps (8%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12404.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12404.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12404.PRE.filtered.fasta jobid: 1703 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12404.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12404.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12404.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12404.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12404.PRE.filtered.gff jobid: 1144 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12404.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12404.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12404.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:51 2023] Finished job 1703. 169 of 2231 steps (8%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:51 2023] Finished job 1144. 170 of 2231 steps (8%) done [Fri Nov 3 10:23:59 2023] Finished job 728. 171 of 2231 steps (8%) done [Fri Nov 3 10:23:59 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-499.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-499.PRE.gff, analyses/output/Amil-MirMachine/Mir-499.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-499.PRE.unfiltered jobid: 727 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-499.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-499.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-499.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:59 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2022.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2022.PRE.result jobid: 300 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2022.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2022.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:23:59 2023] Finished job 727. 172 of 2231 steps (8%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-499.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:23:59 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-499.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-499.PRE.filtered.gff jobid: 1478 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-499.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-499.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-499.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:59 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-499.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-499.PRE.filtered.fasta jobid: 2037 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-499.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-499.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-499.PRE resources: tmpdir=/tmp [Fri Nov 3 10:23:59 2023] Finished job 2037. 173 of 2231 steps (8%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:23:59 2023] Finished job 1478. 174 of 2231 steps (8%) done [Fri Nov 3 10:24:00 2023] Finished job 848. 175 of 2231 steps (8%) done [Fri Nov 3 10:24:00 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-724.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-724.PRE.gff, analyses/output/Amil-MirMachine/Mir-724.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-724.PRE.unfiltered jobid: 847 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-724.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-724.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-724.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:00 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-493.PRE.CM output: analyses/output/Amil-MirMachine/Mir-493.PRE.result jobid: 720 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-493.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-493.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:00 2023] Finished job 847. 176 of 2231 steps (8%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-724.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:00 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-724.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-724.PRE.filtered.gff jobid: 1538 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-724.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-724.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-724.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:00 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-724.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-724.PRE.filtered.fasta jobid: 2097 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-724.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-724.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-724.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:00 2023] Finished job 2097. 177 of 2231 steps (8%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:00 2023] Finished job 1538. 178 of 2231 steps (8%) done [Fri Nov 3 10:24:06 2023] Finished job 720. 179 of 2231 steps (8%) done [Fri Nov 3 10:24:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-143.PRE.CM output: analyses/output/Amil-MirMachine/Mir-143.PRE.result jobid: 128 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-143.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-143.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-493.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-493.PRE.gff, analyses/output/Amil-MirMachine/Mir-493.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-493.PRE.unfiltered jobid: 719 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-493.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-493.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-493.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:06 2023] Finished job 719. 180 of 2231 steps (8%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-493.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-493.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-493.PRE.filtered.gff jobid: 1474 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-493.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-493.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-493.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-493.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-493.PRE.filtered.fasta jobid: 2033 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-493.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-493.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-493.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:06 2023] Finished job 2033. 181 of 2231 steps (8%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:06 2023] Finished job 1474. 182 of 2231 steps (8%) done [Fri Nov 3 10:24:07 2023] Finished job 300. 183 of 2231 steps (8%) done [Fri Nov 3 10:24:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1805.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1805.PRE.result jobid: 188 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1805.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1805.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2022.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2022.PRE.gff, analyses/output/Amil-MirMachine/Mir-2022.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2022.PRE.unfiltered jobid: 299 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2022.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2022.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2022.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:07 2023] Finished job 299. 184 of 2231 steps (8%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2022.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2022.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2022.PRE.filtered.fasta jobid: 1823 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2022.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2022.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2022.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2022.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2022.PRE.filtered.gff jobid: 1264 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2022.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2022.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2022.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:08 2023] Finished job 1823. 185 of 2231 steps (8%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:08 2023] Finished job 1264. 186 of 2231 steps (8%) done [Fri Nov 3 10:24:10 2023] Finished job 128. 187 of 2231 steps (8%) done [Fri Nov 3 10:24:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-143.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-143.PRE.gff, analyses/output/Amil-MirMachine/Mir-143.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-143.PRE.unfiltered jobid: 127 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-143.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-143.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-143.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-789.PRE.CM output: analyses/output/Amil-MirMachine/Mir-789.PRE.result jobid: 960 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-789.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-789.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:10 2023] Finished job 127. 188 of 2231 steps (8%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-143.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-143.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-143.PRE.filtered.gff jobid: 1178 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-143.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-143.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-143.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-143.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-143.PRE.filtered.fasta jobid: 1737 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-143.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-143.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-143.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:11 2023] Finished job 1737. 189 of 2231 steps (8%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:11 2023] Finished job 1178. 190 of 2231 steps (9%) done [Fri Nov 3 10:24:15 2023] Finished job 960. 191 of 2231 steps (9%) done [Fri Nov 3 10:24:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-737.PRE.CM output: analyses/output/Amil-MirMachine/Mir-737.PRE.result jobid: 908 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-737.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-737.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-789.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-789.PRE.gff, analyses/output/Amil-MirMachine/Mir-789.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-789.PRE.unfiltered jobid: 959 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-789.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-789.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-789.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:15 2023] Finished job 959. 192 of 2231 steps (9%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-789.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-789.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-789.PRE.filtered.gff jobid: 1594 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-789.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-789.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-789.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-789.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-789.PRE.filtered.fasta jobid: 2153 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-789.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-789.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-789.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:15 2023] Finished job 2153. 193 of 2231 steps (9%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:16 2023] Finished job 1594. 194 of 2231 steps (9%) done [Fri Nov 3 10:24:16 2023] Finished job 188. 195 of 2231 steps (9%) done [Fri Nov 3 10:24:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1805.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1805.PRE.gff, analyses/output/Amil-MirMachine/Mir-1805.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1805.PRE.unfiltered jobid: 187 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1805.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1805.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1805.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-126.PRE.CM output: analyses/output/Amil-MirMachine/Mir-126.PRE.result jobid: 68 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-126.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-126.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:16 2023] Finished job 187. 196 of 2231 steps (9%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1805.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1805.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1805.PRE.filtered.gff jobid: 1208 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1805.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1805.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1805.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1805.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1805.PRE.filtered.fasta jobid: 1767 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1805.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1805.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1805.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:16 2023] Finished job 1767. 197 of 2231 steps (9%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:17 2023] Finished job 1208. 198 of 2231 steps (9%) done [Fri Nov 3 10:24:21 2023] Finished job 68. 199 of 2231 steps (9%) done [Fri Nov 3 10:24:21 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-126.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-126.PRE.gff, analyses/output/Amil-MirMachine/Mir-126.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-126.PRE.unfiltered jobid: 67 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-126.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-126.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-126.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:21 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-23.PRE.CM output: analyses/output/Amil-MirMachine/Mir-23.PRE.result jobid: 368 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-23.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-23.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:21 2023] Finished job 67. 200 of 2231 steps (9%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-126.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:21 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-126.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-126.PRE.filtered.gff jobid: 1148 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-126.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-126.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-126.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:21 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-126.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-126.PRE.filtered.fasta jobid: 1707 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-126.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-126.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-126.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:21 2023] Finished job 1707. 201 of 2231 steps (9%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:21 2023] Finished job 1148. 202 of 2231 steps (9%) done [Fri Nov 3 10:24:36 2023] Finished job 368. 203 of 2231 steps (9%) done [Fri Nov 3 10:24:36 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-23.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-23.PRE.gff, analyses/output/Amil-MirMachine/Mir-23.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-23.PRE.unfiltered jobid: 367 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-23.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-23.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-23.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:36 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7336.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7336.PRE.result jobid: 900 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7336.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7336.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:36 2023] Finished job 367. 204 of 2231 steps (9%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-23.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:36 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-23.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-23.PRE.filtered.gff jobid: 1298 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-23.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-23.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-23.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:36 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-23.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-23.PRE.filtered.fasta jobid: 1857 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-23.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-23.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-23.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:36 2023] Finished job 1857. 205 of 2231 steps (9%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:37 2023] Finished job 1298. 206 of 2231 steps (9%) done [Fri Nov 3 10:24:40 2023] Finished job 900. 207 of 2231 steps (9%) done [Fri Nov 3 10:24:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2499.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2499.PRE.result jobid: 392 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2499.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2499.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7336.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7336.PRE.gff, analyses/output/Amil-MirMachine/Mir-7336.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7336.PRE.unfiltered jobid: 899 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7336.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7336.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7336.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:40 2023] Finished job 899. 208 of 2231 steps (9%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7336.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7336.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7336.PRE.filtered.fasta jobid: 2123 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7336.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7336.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7336.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7336.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7336.PRE.filtered.gff jobid: 1564 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7336.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7336.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7336.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:40 2023] Finished job 2123. 209 of 2231 steps (9%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:41 2023] Finished job 1564. 210 of 2231 steps (9%) done [Fri Nov 3 10:24:44 2023] Finished job 392. 211 of 2231 steps (9%) done [Fri Nov 3 10:24:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2499.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2499.PRE.gff, analyses/output/Amil-MirMachine/Mir-2499.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2499.PRE.unfiltered jobid: 391 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2499.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2499.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2499.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2687.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2687.PRE.result jobid: 416 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2687.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2687.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] Finished job 908. 212 of 2231 steps (10%) done Select jobs to execute... [Fri Nov 3 10:24:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1993.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1993.PRE.result jobid: 246 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1993.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1993.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-737.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-737.PRE.gff, analyses/output/Amil-MirMachine/Mir-737.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-737.PRE.unfiltered jobid: 907 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-737.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-737.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-737.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] Finished job 391. 213 of 2231 steps (10%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2499.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2499.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2499.PRE.filtered.gff jobid: 1310 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2499.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2499.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2499.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2499.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2499.PRE.filtered.fasta jobid: 1869 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2499.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2499.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2499.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] Finished job 907. 214 of 2231 steps (10%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-737.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-737.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-737.PRE.filtered.gff jobid: 1568 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-737.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-737.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-737.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-737.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-737.PRE.filtered.fasta jobid: 2127 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-737.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-737.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-737.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:44 2023] Finished job 1869. 215 of 2231 steps (10%) done Select jobs to execute... [Fri Nov 3 10:24:44 2023] Finished job 2127. 216 of 2231 steps (10%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:24:45 2023] Finished job 1310. 217 of 2231 steps (10%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:45 2023] Finished job 1568. 218 of 2231 steps (10%) done [Fri Nov 3 10:24:48 2023] Finished job 416. 219 of 2231 steps (10%) done [Fri Nov 3 10:24:48 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-27.PRE.CM output: analyses/output/Amil-MirMachine/Mir-27.PRE.result jobid: 426 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-27.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-27.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:48 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2687.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2687.PRE.gff, analyses/output/Amil-MirMachine/Mir-2687.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2687.PRE.unfiltered jobid: 415 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2687.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2687.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2687.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:48 2023] Finished job 415. 220 of 2231 steps (10%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2687.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:48 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2687.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2687.PRE.filtered.fasta jobid: 1881 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2687.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2687.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2687.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:48 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2687.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2687.PRE.filtered.gff jobid: 1322 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2687.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2687.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2687.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:48 2023] Finished job 1881. 221 of 2231 steps (10%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:48 2023] Finished job 1322. 222 of 2231 steps (10%) done [Fri Nov 3 10:24:52 2023] Finished job 246. 223 of 2231 steps (10%) done [Fri Nov 3 10:24:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1993.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1993.PRE.gff, analyses/output/Amil-MirMachine/Mir-1993.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1993.PRE.unfiltered jobid: 245 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1993.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1993.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1993.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-86.PRE.CM output: analyses/output/Amil-MirMachine/Mir-86.PRE.result jobid: 970 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-86.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-86.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:53 2023] Finished job 245. 224 of 2231 steps (10%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1993.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1993.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1993.PRE.filtered.fasta jobid: 1796 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1993.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1993.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1993.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1993.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1993.PRE.filtered.gff jobid: 1237 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1993.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1993.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1993.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:53 2023] Finished job 1796. 225 of 2231 steps (10%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:53 2023] Finished job 1237. 226 of 2231 steps (10%) done [Fri Nov 3 10:24:56 2023] Finished job 426. 227 of 2231 steps (10%) done [Fri Nov 3 10:24:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-27.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-27.PRE.gff, analyses/output/Amil-MirMachine/Mir-27.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-27.PRE.unfiltered jobid: 425 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-27.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-27.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-27.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-452.PRE.CM output: analyses/output/Amil-MirMachine/Mir-452.PRE.result jobid: 610 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-452.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-452.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:24:57 2023] Finished job 425. 228 of 2231 steps (10%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-27.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:24:57 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-27.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-27.PRE.filtered.gff jobid: 1327 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-27.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-27.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-27.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:57 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-27.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-27.PRE.filtered.fasta jobid: 1886 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-27.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-27.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-27.PRE resources: tmpdir=/tmp [Fri Nov 3 10:24:57 2023] Finished job 1886. 229 of 2231 steps (10%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:24:57 2023] Finished job 1327. 230 of 2231 steps (10%) done [Fri Nov 3 10:25:01 2023] Finished job 970. 231 of 2231 steps (10%) done [Fri Nov 3 10:25:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4839.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4839.PRE.result jobid: 666 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4839.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4839.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-86.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-86.PRE.gff, analyses/output/Amil-MirMachine/Mir-86.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-86.PRE.unfiltered jobid: 969 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-86.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-86.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-86.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:01 2023] Finished job 969. 232 of 2231 steps (10%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-86.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-86.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-86.PRE.filtered.gff jobid: 1599 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-86.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-86.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-86.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-86.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-86.PRE.filtered.fasta jobid: 2158 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-86.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-86.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-86.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:01 2023] Finished job 2158. 233 of 2231 steps (10%) done Select jobs to execute... [Fri Nov 3 10:25:01 2023] Finished job 610. 234 of 2231 steps (10%) done [Fri Nov 3 10:25:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-452.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-452.PRE.gff, analyses/output/Amil-MirMachine/Mir-452.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-452.PRE.unfiltered jobid: 609 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-452.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-452.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-452.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7246.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7246.PRE.result jobid: 850 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7246.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7246.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:01 2023] Finished job 609. 235 of 2231 steps (11%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-452.PRE.ext.gff. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:25:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-452.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-452.PRE.filtered.gff jobid: 1419 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-452.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-452.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-452.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-452.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-452.PRE.filtered.fasta jobid: 1978 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-452.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-452.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-452.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:02 2023] Finished job 1978. 236 of 2231 steps (11%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:02 2023] Finished job 1599. 237 of 2231 steps (11%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:02 2023] Finished job 1419. 238 of 2231 steps (11%) done [Fri Nov 3 10:25:08 2023] Finished job 850. 239 of 2231 steps (11%) done [Fri Nov 3 10:25:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7246.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7246.PRE.gff, analyses/output/Amil-MirMachine/Mir-7246.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7246.PRE.unfiltered jobid: 849 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7246.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7246.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7246.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Lsy-6.PRE.CM output: analyses/output/Amil-MirMachine/Lsy-6.PRE.result jobid: 10 reason: Missing output files: analyses/output/Amil-MirMachine/Lsy-6.PRE.result wildcards: species=Amil-MirMachine, mirna=Lsy-6.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:08 2023] Finished job 849. 240 of 2231 steps (11%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7246.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7246.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7246.PRE.filtered.gff jobid: 1539 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7246.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7246.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7246.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7246.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7246.PRE.filtered.fasta jobid: 2098 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7246.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7246.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7246.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:08 2023] Finished job 2098. 241 of 2231 steps (11%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:08 2023] Finished job 1539. 242 of 2231 steps (11%) done [Fri Nov 3 10:25:09 2023] Finished job 666. 243 of 2231 steps (11%) done [Fri Nov 3 10:25:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4839.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4839.PRE.gff, analyses/output/Amil-MirMachine/Mir-4839.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4839.PRE.unfiltered jobid: 665 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4839.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4839.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4839.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-504.PRE.CM output: analyses/output/Amil-MirMachine/Mir-504.PRE.result jobid: 730 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-504.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-504.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:09 2023] Finished job 665. 244 of 2231 steps (11%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4839.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4839.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4839.PRE.filtered.gff jobid: 1447 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4839.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4839.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4839.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4839.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4839.PRE.filtered.fasta jobid: 2006 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4839.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4839.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4839.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:09 2023] Finished job 2006. 245 of 2231 steps (11%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:09 2023] Finished job 1447. 246 of 2231 steps (11%) done [Fri Nov 3 10:25:15 2023] Finished job 730. 247 of 2231 steps (11%) done [Fri Nov 3 10:25:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-504.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-504.PRE.gff, analyses/output/Amil-MirMachine/Mir-504.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-504.PRE.unfiltered jobid: 729 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-504.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-504.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-504.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-144.PRE.CM output: analyses/output/Amil-MirMachine/Mir-144.PRE.result jobid: 130 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-144.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-144.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:15 2023] Finished job 729. 248 of 2231 steps (11%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-504.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-504.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-504.PRE.filtered.gff jobid: 1479 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-504.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-504.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-504.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-504.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-504.PRE.filtered.fasta jobid: 2038 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-504.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-504.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-504.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:15 2023] Finished job 2038. 249 of 2231 steps (11%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:15 2023] Finished job 1479. 250 of 2231 steps (11%) done [Fri Nov 3 10:25:20 2023] Finished job 10. 251 of 2231 steps (11%) done [Fri Nov 3 10:25:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Lsy-6.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Lsy-6.PRE.gff, analyses/output/Amil-MirMachine/Lsy-6.PRE.ext.gff, analyses/output/Amil-MirMachine/Lsy-6.PRE.unfiltered jobid: 9 reason: Missing output files: analyses/output/Amil-MirMachine/Lsy-6.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Lsy-6.PRE.result wildcards: species=Amil-MirMachine, mirna=Lsy-6.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2056.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2056.PRE.result jobid: 310 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2056.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2056.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:20 2023] Finished job 9. 252 of 2231 steps (11%) done Removing temporary output analyses/output/Amil-MirMachine/Lsy-6.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Lsy-6.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Lsy-6.PRE.filtered.fasta jobid: 1678 reason: Missing output files: analyses/output/Amil-MirMachine/Lsy-6.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Lsy-6.PRE.gff wildcards: species=Amil-MirMachine, mirna=Lsy-6.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Lsy-6.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Lsy-6.PRE.filtered.gff jobid: 1119 reason: Missing output files: analyses/output/Amil-MirMachine/Lsy-6.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Lsy-6.PRE.gff wildcards: species=Amil-MirMachine, mirna=Lsy-6.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:20 2023] Finished job 1678. 253 of 2231 steps (11%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:20 2023] Finished job 1119. 254 of 2231 steps (11%) done [Fri Nov 3 10:25:23 2023] Finished job 130. 255 of 2231 steps (11%) done [Fri Nov 3 10:25:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-144.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-144.PRE.gff, analyses/output/Amil-MirMachine/Mir-144.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-144.PRE.unfiltered jobid: 129 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-144.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-144.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-144.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-181.PRE.CM output: analyses/output/Amil-MirMachine/Mir-181.PRE.result jobid: 190 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-181.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-181.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] Finished job 310. 256 of 2231 steps (11%) done Select jobs to execute... [Fri Nov 3 10:25:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2056.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2056.PRE.gff, analyses/output/Amil-MirMachine/Mir-2056.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2056.PRE.unfiltered jobid: 309 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2056.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2056.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2056.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7370.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7370.PRE.result jobid: 910 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7370.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7370.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] Finished job 129. 257 of 2231 steps (12%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-144.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-144.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-144.PRE.filtered.gff jobid: 1179 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-144.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-144.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-144.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-144.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-144.PRE.filtered.fasta jobid: 1738 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-144.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-144.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-144.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] Finished job 309. 258 of 2231 steps (12%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2056.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2056.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2056.PRE.filtered.gff jobid: 1269 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2056.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2056.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2056.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2056.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2056.PRE.filtered.fasta jobid: 1828 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2056.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2056.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2056.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:23 2023] Finished job 1738. 259 of 2231 steps (12%) done Select jobs to execute... [Fri Nov 3 10:25:24 2023] Finished job 1828. 260 of 2231 steps (12%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:25:24 2023] Finished job 1179. 261 of 2231 steps (12%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:24 2023] Finished job 1269. 262 of 2231 steps (12%) done [Fri Nov 3 10:25:29 2023] Finished job 190. 263 of 2231 steps (12%) done [Fri Nov 3 10:25:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-181.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-181.PRE.gff, analyses/output/Amil-MirMachine/Mir-181.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-181.PRE.unfiltered jobid: 189 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-181.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-181.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-181.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-127.PRE.CM output: analyses/output/Amil-MirMachine/Mir-127.PRE.result jobid: 70 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-127.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-127.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:29 2023] Finished job 189. 264 of 2231 steps (12%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-181.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-181.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-181.PRE.filtered.gff jobid: 1209 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-181.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-181.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-181.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-181.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-181.PRE.filtered.fasta jobid: 1768 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-181.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-181.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-181.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:29 2023] Finished job 1768. 265 of 2231 steps (12%) done Select jobs to execute... [Fri Nov 3 10:25:29 2023] Finished job 910. 266 of 2231 steps (12%) done [Fri Nov 3 10:25:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1720.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1720.PRE.result jobid: 180 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1720.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1720.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7370.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7370.PRE.gff, analyses/output/Amil-MirMachine/Mir-7370.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7370.PRE.unfiltered jobid: 909 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7370.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7370.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7370.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:25:29 2023] Finished job 909. 267 of 2231 steps (12%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7370.PRE.ext.gff. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7370.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7370.PRE.filtered.gff jobid: 1569 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7370.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7370.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7370.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7370.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7370.PRE.filtered.fasta jobid: 2128 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7370.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7370.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7370.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:29 2023] Finished job 1209. 268 of 2231 steps (12%) done Select jobs to execute... [Fri Nov 3 10:25:29 2023] Finished job 2128. 269 of 2231 steps (12%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:30 2023] Finished job 1569. 270 of 2231 steps (12%) done [Fri Nov 3 10:25:32 2023] Finished job 70. 271 of 2231 steps (12%) done [Fri Nov 3 10:25:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-127.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-127.PRE.gff, analyses/output/Amil-MirMachine/Mir-127.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-127.PRE.unfiltered jobid: 69 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-127.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-127.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-127.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-230.PRE.CM output: analyses/output/Amil-MirMachine/Mir-230.PRE.result jobid: 370 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-230.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-230.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:32 2023] Finished job 69. 272 of 2231 steps (12%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-127.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-127.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-127.PRE.filtered.gff jobid: 1149 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-127.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-127.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-127.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-127.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-127.PRE.filtered.fasta jobid: 1708 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-127.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-127.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-127.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:32 2023] Finished job 1708. 273 of 2231 steps (12%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:33 2023] Finished job 1149. 274 of 2231 steps (12%) done [Fri Nov 3 10:25:36 2023] Finished job 180. 275 of 2231 steps (12%) done [Fri Nov 3 10:25:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4524.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4524.PRE.result jobid: 612 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4524.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4524.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1720.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1720.PRE.gff, analyses/output/Amil-MirMachine/Mir-1720.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1720.PRE.unfiltered jobid: 179 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1720.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1720.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1720.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:37 2023] Finished job 179. 276 of 2231 steps (12%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1720.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1720.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1720.PRE.filtered.fasta jobid: 1763 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1720.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1720.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1720.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1720.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1720.PRE.filtered.gff jobid: 1204 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1720.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1720.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1720.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:37 2023] Finished job 1763. 277 of 2231 steps (12%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:37 2023] Finished job 1204. 278 of 2231 steps (12%) done [Fri Nov 3 10:25:39 2023] Finished job 370. 279 of 2231 steps (13%) done [Fri Nov 3 10:25:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7247.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7247.PRE.result jobid: 852 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7247.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7247.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-230.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-230.PRE.gff, analyses/output/Amil-MirMachine/Mir-230.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-230.PRE.unfiltered jobid: 369 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-230.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-230.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-230.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:39 2023] Finished job 369. 280 of 2231 steps (13%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-230.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-230.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-230.PRE.filtered.gff jobid: 1299 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-230.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-230.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-230.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-230.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-230.PRE.filtered.fasta jobid: 1858 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-230.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-230.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-230.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:40 2023] Finished job 1858. 281 of 2231 steps (13%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:40 2023] Finished job 1299. 282 of 2231 steps (13%) done [Fri Nov 3 10:25:41 2023] Finished job 612. 283 of 2231 steps (13%) done [Fri Nov 3 10:25:41 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-14.PRE.CM output: analyses/output/Amil-MirMachine/Mir-14.PRE.result jobid: 120 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-14.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-14.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:41 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4524.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4524.PRE.gff, analyses/output/Amil-MirMachine/Mir-4524.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4524.PRE.unfiltered jobid: 611 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4524.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4524.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4524.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:41 2023] Finished job 611. 284 of 2231 steps (13%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4524.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:41 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4524.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4524.PRE.filtered.fasta jobid: 1979 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4524.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4524.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4524.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:41 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4524.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4524.PRE.filtered.gff jobid: 1420 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4524.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4524.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4524.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:42 2023] Finished job 1979. 285 of 2231 steps (13%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:42 2023] Finished job 1420. 286 of 2231 steps (13%) done [Fri Nov 3 10:25:42 2023] Finished job 852. 287 of 2231 steps (13%) done [Fri Nov 3 10:25:42 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-231.PRE.CM output: analyses/output/Amil-MirMachine/Mir-231.PRE.result jobid: 372 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-231.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-231.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:42 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7247.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7247.PRE.gff, analyses/output/Amil-MirMachine/Mir-7247.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7247.PRE.unfiltered jobid: 851 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7247.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7247.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7247.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:42 2023] Finished job 851. 288 of 2231 steps (13%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7247.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7247.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7247.PRE.filtered.fasta jobid: 2099 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7247.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7247.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7247.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7247.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7247.PRE.filtered.gff jobid: 1540 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7247.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7247.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7247.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:43 2023] Finished job 2099. 289 of 2231 steps (13%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:43 2023] Finished job 1540. 290 of 2231 steps (13%) done [Fri Nov 3 10:25:49 2023] Finished job 120. 291 of 2231 steps (13%) done [Fri Nov 3 10:25:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1817.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1817.PRE.result jobid: 192 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1817.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1817.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-14.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-14.PRE.gff, analyses/output/Amil-MirMachine/Mir-14.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-14.PRE.unfiltered jobid: 119 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-14.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-14.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-14.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:49 2023] Finished job 119. 292 of 2231 steps (13%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-14.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-14.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-14.PRE.filtered.gff jobid: 1174 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-14.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-14.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-14.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-14.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-14.PRE.filtered.fasta jobid: 1733 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-14.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-14.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-14.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:49 2023] Finished job 1733. 293 of 2231 steps (13%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:49 2023] Finished job 1174. 294 of 2231 steps (13%) done [Fri Nov 3 10:25:52 2023] Finished job 372. 295 of 2231 steps (13%) done [Fri Nov 3 10:25:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7371.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7371.PRE.result jobid: 912 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7371.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7371.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:25:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-231.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-231.PRE.gff, analyses/output/Amil-MirMachine/Mir-231.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-231.PRE.unfiltered jobid: 371 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-231.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-231.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-231.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:53 2023] Finished job 371. 296 of 2231 steps (13%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-231.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:25:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-231.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-231.PRE.filtered.fasta jobid: 1859 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-231.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-231.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-231.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-231.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-231.PRE.filtered.gff jobid: 1300 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-231.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-231.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-231.PRE resources: tmpdir=/tmp [Fri Nov 3 10:25:53 2023] Finished job 1859. 297 of 2231 steps (13%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:25:53 2023] Finished job 1300. 298 of 2231 steps (13%) done [Fri Nov 3 10:26:01 2023] Finished job 192. 299 of 2231 steps (13%) done [Fri Nov 3 10:26:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7149.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7149.PRE.result jobid: 840 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7149.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7149.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1817.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1817.PRE.gff, analyses/output/Amil-MirMachine/Mir-1817.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1817.PRE.unfiltered jobid: 191 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1817.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1817.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1817.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:01 2023] Finished job 191. 300 of 2231 steps (13%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1817.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1817.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1817.PRE.filtered.gff jobid: 1210 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1817.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1817.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1817.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1817.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1817.PRE.filtered.fasta jobid: 1769 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1817.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1817.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1817.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:01 2023] Finished job 1769. 301 of 2231 steps (13%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:01 2023] Finished job 1210. 302 of 2231 steps (14%) done [Fri Nov 3 10:26:07 2023] Finished job 840. 303 of 2231 steps (14%) done [Fri Nov 3 10:26:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-145.PRE.CM output: analyses/output/Amil-MirMachine/Mir-145.PRE.result jobid: 132 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-145.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-145.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7149.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7149.PRE.gff, analyses/output/Amil-MirMachine/Mir-7149.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7149.PRE.unfiltered jobid: 839 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7149.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7149.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7149.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:07 2023] Finished job 839. 304 of 2231 steps (14%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7149.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7149.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7149.PRE.filtered.gff jobid: 1534 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7149.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7149.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7149.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7149.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7149.PRE.filtered.fasta jobid: 2093 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7149.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7149.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7149.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:07 2023] Finished job 2093. 305 of 2231 steps (14%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:08 2023] Finished job 1534. 306 of 2231 steps (14%) done [Fri Nov 3 10:26:09 2023] Finished job 912. 307 of 2231 steps (14%) done [Fri Nov 3 10:26:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1271.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1271.PRE.result jobid: 72 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1271.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1271.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7371.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7371.PRE.gff, analyses/output/Amil-MirMachine/Mir-7371.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7371.PRE.unfiltered jobid: 911 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7371.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7371.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7371.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:09 2023] Finished job 911. 308 of 2231 steps (14%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7371.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7371.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7371.PRE.filtered.gff jobid: 1570 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7371.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7371.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7371.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7371.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7371.PRE.filtered.fasta jobid: 2129 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7371.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7371.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7371.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:09 2023] Finished job 2129. 309 of 2231 steps (14%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:09 2023] Finished job 1570. 310 of 2231 steps (14%) done [Fri Nov 3 10:26:14 2023] Finished job 132. 311 of 2231 steps (14%) done [Fri Nov 3 10:26:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-87.PRE.CM output: analyses/output/Amil-MirMachine/Mir-87.PRE.result jobid: 972 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-87.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-87.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-145.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-145.PRE.gff, analyses/output/Amil-MirMachine/Mir-145.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-145.PRE.unfiltered jobid: 131 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-145.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-145.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-145.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:15 2023] Finished job 131. 312 of 2231 steps (14%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-145.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-145.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-145.PRE.filtered.fasta jobid: 1739 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-145.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-145.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-145.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-145.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-145.PRE.filtered.gff jobid: 1180 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-145.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-145.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-145.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:15 2023] Finished job 1739. 313 of 2231 steps (14%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:15 2023] Finished job 1180. 314 of 2231 steps (14%) done [Fri Nov 3 10:26:16 2023] Finished job 72. 315 of 2231 steps (14%) done [Fri Nov 3 10:26:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-432.PRE.CM output: analyses/output/Amil-MirMachine/Mir-432.PRE.result jobid: 600 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-432.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-432.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1271.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1271.PRE.gff, analyses/output/Amil-MirMachine/Mir-1271.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1271.PRE.unfiltered jobid: 71 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1271.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1271.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1271.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:16 2023] Finished job 71. 316 of 2231 steps (14%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1271.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1271.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1271.PRE.filtered.gff jobid: 1150 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1271.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1271.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1271.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1271.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1271.PRE.filtered.fasta jobid: 1709 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1271.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1271.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1271.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:16 2023] Finished job 1709. 317 of 2231 steps (14%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:16 2023] Finished job 1150. 318 of 2231 steps (14%) done [Fri Nov 3 10:26:22 2023] Finished job 600. 319 of 2231 steps (14%) done [Fri Nov 3 10:26:22 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-505.PRE.CM output: analyses/output/Amil-MirMachine/Mir-505.PRE.result jobid: 732 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-505.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-505.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:22 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-432.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-432.PRE.gff, analyses/output/Amil-MirMachine/Mir-432.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-432.PRE.unfiltered jobid: 599 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-432.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-432.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-432.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:22 2023] Finished job 599. 320 of 2231 steps (14%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-432.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:22 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-432.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-432.PRE.filtered.gff jobid: 1414 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-432.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-432.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-432.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:22 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-432.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-432.PRE.filtered.fasta jobid: 1973 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-432.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-432.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-432.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:22 2023] Finished job 1973. 321 of 2231 steps (14%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:22 2023] Finished job 1414. 322 of 2231 steps (14%) done [Fri Nov 3 10:26:23 2023] Finished job 972. 323 of 2231 steps (14%) done [Fri Nov 3 10:26:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1.PRE.result jobid: 12 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-87.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-87.PRE.gff, analyses/output/Amil-MirMachine/Mir-87.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-87.PRE.unfiltered jobid: 971 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-87.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-87.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-87.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:23 2023] Finished job 971. 324 of 2231 steps (15%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-87.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-87.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-87.PRE.filtered.fasta jobid: 2159 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-87.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-87.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-87.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-87.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-87.PRE.filtered.gff jobid: 1600 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-87.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-87.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-87.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:23 2023] Finished job 2159. 325 of 2231 steps (15%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:23 2023] Finished job 1600. 326 of 2231 steps (15%) done [Fri Nov 3 10:26:26 2023] Finished job 732. 327 of 2231 steps (15%) done [Fri Nov 3 10:26:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2057.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2057.PRE.result jobid: 312 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2057.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2057.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-505.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-505.PRE.gff, analyses/output/Amil-MirMachine/Mir-505.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-505.PRE.unfiltered jobid: 731 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-505.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-505.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-505.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:26 2023] Finished job 731. 328 of 2231 steps (15%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-505.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-505.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-505.PRE.filtered.fasta jobid: 2039 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-505.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-505.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-505.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-505.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-505.PRE.filtered.gff jobid: 1480 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-505.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-505.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-505.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:26 2023] Finished job 2039. 329 of 2231 steps (15%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:26 2023] Finished job 1480. 330 of 2231 steps (15%) done [Fri Nov 3 10:26:29 2023] Finished job 312. 331 of 2231 steps (15%) done [Fri Nov 3 10:26:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2686.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2686.PRE.result jobid: 414 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2686.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2686.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2057.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2057.PRE.gff, analyses/output/Amil-MirMachine/Mir-2057.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2057.PRE.unfiltered jobid: 311 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2057.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2057.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2057.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:29 2023] Finished job 311. 332 of 2231 steps (15%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2057.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2057.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2057.PRE.filtered.gff jobid: 1270 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2057.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2057.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2057.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2057.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2057.PRE.filtered.fasta jobid: 1829 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2057.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2057.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2057.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:29 2023] Finished job 1829. 333 of 2231 steps (15%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:30 2023] Finished job 1270. 334 of 2231 steps (15%) done [Fri Nov 3 10:26:30 2023] Finished job 12. 335 of 2231 steps (15%) done [Fri Nov 3 10:26:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2058.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2058.PRE.result jobid: 314 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2058.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2058.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1.PRE.gff, analyses/output/Amil-MirMachine/Mir-1.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1.PRE.unfiltered jobid: 11 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:30 2023] Finished job 11. 336 of 2231 steps (15%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1.PRE.filtered.fasta jobid: 1679 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1.PRE.filtered.gff jobid: 1120 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:30 2023] Finished job 1679. 337 of 2231 steps (15%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:31 2023] Finished job 1120. 338 of 2231 steps (15%) done [Fri Nov 3 10:26:34 2023] Finished job 314. 339 of 2231 steps (15%) done [Fri Nov 3 10:26:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2058.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2058.PRE.gff, analyses/output/Amil-MirMachine/Mir-2058.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2058.PRE.unfiltered jobid: 313 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2058.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2058.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2058.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-10.PRE.CM output: analyses/output/Amil-MirMachine/Mir-10.PRE.result jobid: 14 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-10.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-10.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:34 2023] Finished job 313. 340 of 2231 steps (15%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2058.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2058.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2058.PRE.filtered.gff jobid: 1271 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2058.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2058.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2058.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2058.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2058.PRE.filtered.fasta jobid: 1830 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2058.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2058.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2058.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:34 2023] Finished job 1830. 341 of 2231 steps (15%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:34 2023] Finished job 1271. 342 of 2231 steps (15%) done [Fri Nov 3 10:26:37 2023] Finished job 414. 343 of 2231 steps (15%) done [Fri Nov 3 10:26:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2686.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2686.PRE.gff, analyses/output/Amil-MirMachine/Mir-2686.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2686.PRE.unfiltered jobid: 413 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2686.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2686.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2686.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1277.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1277.PRE.result jobid: 74 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1277.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1277.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:37 2023] Finished job 413. 344 of 2231 steps (15%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2686.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2686.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2686.PRE.filtered.fasta jobid: 1880 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2686.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2686.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2686.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2686.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2686.PRE.filtered.gff jobid: 1321 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2686.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2686.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2686.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:37 2023] Finished job 1880. 345 of 2231 steps (15%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:37 2023] Finished job 1321. 346 of 2231 steps (16%) done [Fri Nov 3 10:26:39 2023] Finished job 14. 347 of 2231 steps (16%) done [Fri Nov 3 10:26:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-957.PRE.CM output: analyses/output/Amil-MirMachine/Mir-957.PRE.result jobid: 1024 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-957.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-957.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-10.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-10.PRE.gff, analyses/output/Amil-MirMachine/Mir-10.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-10.PRE.unfiltered jobid: 13 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-10.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-10.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-10.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:39 2023] Finished job 13. 348 of 2231 steps (16%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-10.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-10.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-10.PRE.filtered.gff jobid: 1121 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-10.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-10.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-10.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-10.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-10.PRE.filtered.fasta jobid: 1680 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-10.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-10.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-10.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:39 2023] Finished job 1680. 349 of 2231 steps (16%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:39 2023] Finished job 1121. 350 of 2231 steps (16%) done [Fri Nov 3 10:26:47 2023] Finished job 1024. 351 of 2231 steps (16%) done [Fri Nov 3 10:26:47 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2355.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2355.PRE.result jobid: 374 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2355.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2355.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:26:47 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-957.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-957.PRE.gff, analyses/output/Amil-MirMachine/Mir-957.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-957.PRE.unfiltered jobid: 1023 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-957.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-957.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-957.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:47 2023] Finished job 1023. 352 of 2231 steps (16%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-957.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:26:48 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-957.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-957.PRE.filtered.gff jobid: 1626 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-957.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-957.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-957.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:48 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-957.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-957.PRE.filtered.fasta jobid: 2185 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-957.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-957.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-957.PRE resources: tmpdir=/tmp [Fri Nov 3 10:26:48 2023] Finished job 2185. 353 of 2231 steps (16%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:26:48 2023] Finished job 1626. 354 of 2231 steps (16%) done [Fri Nov 3 10:27:00 2023] Finished job 374. 355 of 2231 steps (16%) done [Fri Nov 3 10:27:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2355.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2355.PRE.gff, analyses/output/Amil-MirMachine/Mir-2355.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2355.PRE.unfiltered jobid: 373 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2355.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2355.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4541.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4541.PRE.result jobid: 614 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4541.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4541.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:01 2023] Finished job 373. 356 of 2231 steps (16%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2355.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2355.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2355.PRE.filtered.gff jobid: 1301 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2355.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2355.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2355.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2355.PRE.filtered.fasta jobid: 1860 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2355.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2355.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:01 2023] Finished job 1860. 357 of 2231 steps (16%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:01 2023] Finished job 1301. 358 of 2231 steps (16%) done [Fri Nov 3 10:27:10 2023] Finished job 614. 359 of 2231 steps (16%) done [Fri Nov 3 10:27:11 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4541.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4541.PRE.gff, analyses/output/Amil-MirMachine/Mir-4541.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4541.PRE.unfiltered jobid: 613 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4541.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4541.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:11 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-725.PRE.CM output: analyses/output/Amil-MirMachine/Mir-725.PRE.result jobid: 854 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-725.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-725.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:11 2023] Finished job 613. 360 of 2231 steps (16%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4541.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4541.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4541.PRE.filtered.gff jobid: 1421 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4541.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4541.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4541.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4541.PRE.filtered.fasta jobid: 1980 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4541.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4541.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:11 2023] Finished job 1980. 361 of 2231 steps (16%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:11 2023] Finished job 1421. 362 of 2231 steps (16%) done [Fri Nov 3 10:27:12 2023] Finished job 74. 363 of 2231 steps (16%) done [Fri Nov 3 10:27:12 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1277.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1277.PRE.gff, analyses/output/Amil-MirMachine/Mir-1277.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1277.PRE.unfiltered jobid: 73 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1277.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1277.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1277.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:12 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-624.PRE.CM output: analyses/output/Amil-MirMachine/Mir-624.PRE.result jobid: 786 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-624.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-624.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:13 2023] Finished job 73. 364 of 2231 steps (16%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1277.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1277.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1277.PRE.filtered.gff jobid: 1151 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1277.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1277.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1277.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1277.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1277.PRE.filtered.fasta jobid: 1710 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1277.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1277.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1277.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:13 2023] Finished job 1710. 365 of 2231 steps (16%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:13 2023] Finished job 1151. 366 of 2231 steps (16%) done [Fri Nov 3 10:27:17 2023] Finished job 786. 367 of 2231 steps (16%) done [Fri Nov 3 10:27:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-624.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-624.PRE.gff, analyses/output/Amil-MirMachine/Mir-624.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-624.PRE.unfiltered jobid: 785 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-624.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-624.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-624.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1451.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1451.PRE.result jobid: 134 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1451.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1451.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:17 2023] Finished job 785. 368 of 2231 steps (16%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-624.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-624.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-624.PRE.filtered.fasta jobid: 2066 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-624.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-624.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-624.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-624.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-624.PRE.filtered.gff jobid: 1507 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-624.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-624.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-624.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:17 2023] Finished job 2066. 369 of 2231 steps (17%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:18 2023] Finished job 1507. 370 of 2231 steps (17%) done [Fri Nov 3 10:27:19 2023] Finished job 854. 371 of 2231 steps (17%) done [Fri Nov 3 10:27:19 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-725.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-725.PRE.gff, analyses/output/Amil-MirMachine/Mir-725.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-725.PRE.unfiltered jobid: 853 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-725.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-725.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-725.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:19 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-959.PRE.CM output: analyses/output/Amil-MirMachine/Mir-959.PRE.result jobid: 1026 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-959.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-959.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:19 2023] Finished job 853. 372 of 2231 steps (17%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-725.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-725.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-725.PRE.filtered.gff jobid: 1541 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-725.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-725.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-725.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-725.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-725.PRE.filtered.fasta jobid: 2100 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-725.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-725.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-725.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:20 2023] Finished job 2100. 373 of 2231 steps (17%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:20 2023] Finished job 1541. 374 of 2231 steps (17%) done [Fri Nov 3 10:27:20 2023] Finished job 134. 375 of 2231 steps (17%) done [Fri Nov 3 10:27:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1451.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1451.PRE.gff, analyses/output/Amil-MirMachine/Mir-1451.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1451.PRE.unfiltered jobid: 133 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1451.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1451.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1451.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-977.PRE.CM output: analyses/output/Amil-MirMachine/Mir-977.PRE.result jobid: 1086 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-977.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-977.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:21 2023] Finished job 133. 376 of 2231 steps (17%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1451.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:21 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1451.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1451.PRE.filtered.gff jobid: 1181 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1451.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1451.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1451.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:21 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1451.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1451.PRE.filtered.fasta jobid: 1740 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1451.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1451.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1451.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:21 2023] Finished job 1740. 377 of 2231 steps (17%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:21 2023] Finished job 1181. 378 of 2231 steps (17%) done [Fri Nov 3 10:27:23 2023] Finished job 1026. 379 of 2231 steps (17%) done [Fri Nov 3 10:27:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-959.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-959.PRE.gff, analyses/output/Amil-MirMachine/Mir-959.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-959.PRE.unfiltered jobid: 1025 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-959.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-959.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-959.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7373.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7373.PRE.result jobid: 914 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7373.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7373.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:23 2023] Finished job 1025. 380 of 2231 steps (17%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-959.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-959.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-959.PRE.filtered.gff jobid: 1627 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-959.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-959.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-959.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-959.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-959.PRE.filtered.fasta jobid: 2186 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-959.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-959.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-959.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:23 2023] Finished job 2186. 381 of 2231 steps (17%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:23 2023] Finished job 1627. 382 of 2231 steps (17%) done [Fri Nov 3 10:27:29 2023] Finished job 1086. 383 of 2231 steps (17%) done [Fri Nov 3 10:27:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-872.PRE.CM output: analyses/output/Amil-MirMachine/Mir-872.PRE.result jobid: 974 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-872.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-872.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-977.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-977.PRE.gff, analyses/output/Amil-MirMachine/Mir-977.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-977.PRE.unfiltered jobid: 1085 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-977.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-977.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-977.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:29 2023] Finished job 1085. 384 of 2231 steps (17%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-977.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-977.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-977.PRE.filtered.fasta jobid: 2216 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-977.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-977.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-977.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-977.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-977.PRE.filtered.gff jobid: 1657 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-977.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-977.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-977.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:29 2023] Finished job 2216. 385 of 2231 steps (17%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:29 2023] Finished job 1657. 386 of 2231 steps (17%) done [Fri Nov 3 10:27:34 2023] Finished job 914. 387 of 2231 steps (17%) done [Fri Nov 3 10:27:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7373.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7373.PRE.gff, analyses/output/Amil-MirMachine/Mir-7373.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7373.PRE.unfiltered jobid: 913 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7373.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7373.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7373.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-511.PRE.CM output: analyses/output/Amil-MirMachine/Mir-511.PRE.result jobid: 736 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-511.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-511.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:34 2023] Finished job 913. 388 of 2231 steps (17%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7373.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7373.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7373.PRE.filtered.gff jobid: 1571 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7373.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7373.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7373.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7373.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7373.PRE.filtered.fasta jobid: 2130 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7373.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7373.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7373.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:34 2023] Finished job 2130. 389 of 2231 steps (17%) done Select jobs to execute... [Fri Nov 3 10:27:34 2023] Finished job 974. 390 of 2231 steps (17%) done [Fri Nov 3 10:27:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-872.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-872.PRE.gff, analyses/output/Amil-MirMachine/Mir-872.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-872.PRE.unfiltered jobid: 973 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-872.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-872.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-872.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1000.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1000.PRE.result jobid: 16 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1000.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1000.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:34 2023] Finished job 973. 391 of 2231 steps (18%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-872.PRE.ext.gff. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:27:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-872.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-872.PRE.filtered.gff jobid: 1601 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-872.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-872.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-872.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-872.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-872.PRE.filtered.fasta jobid: 2160 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-872.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-872.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-872.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:35 2023] Finished job 2160. 392 of 2231 steps (18%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:35 2023] Finished job 1571. 393 of 2231 steps (18%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:35 2023] Finished job 1601. 394 of 2231 steps (18%) done [Fri Nov 3 10:27:41 2023] Finished job 16. 395 of 2231 steps (18%) done [Fri Nov 3 10:27:41 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-506.PRE.CM output: analyses/output/Amil-MirMachine/Mir-506.PRE.result jobid: 734 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-506.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-506.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:41 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1000.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1000.PRE.gff, analyses/output/Amil-MirMachine/Mir-1000.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1000.PRE.unfiltered jobid: 15 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1000.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1000.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1000.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:41 2023] Finished job 15. 396 of 2231 steps (18%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1000.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:41 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1000.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1000.PRE.filtered.gff jobid: 1122 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1000.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1000.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1000.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:41 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1000.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1000.PRE.filtered.fasta jobid: 1681 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1000.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1000.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1000.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:41 2023] Finished job 1681. 397 of 2231 steps (18%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:42 2023] Finished job 1122. 398 of 2231 steps (18%) done [Fri Nov 3 10:27:46 2023] Finished job 736. 399 of 2231 steps (18%) done [Fri Nov 3 10:27:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-511.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-511.PRE.gff, analyses/output/Amil-MirMachine/Mir-511.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-511.PRE.unfiltered jobid: 735 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-511.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-511.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-511.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-873.PRE.CM output: analyses/output/Amil-MirMachine/Mir-873.PRE.result jobid: 976 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-873.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-873.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:46 2023] Finished job 735. 400 of 2231 steps (18%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-511.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-511.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-511.PRE.filtered.gff jobid: 1482 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-511.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-511.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-511.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-511.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-511.PRE.filtered.fasta jobid: 2041 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-511.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-511.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-511.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:46 2023] Finished job 2041. 401 of 2231 steps (18%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:46 2023] Finished job 1482. 402 of 2231 steps (18%) done [Fri Nov 3 10:27:51 2023] Finished job 976. 403 of 2231 steps (18%) done [Fri Nov 3 10:27:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-184.PRE.CM output: analyses/output/Amil-MirMachine/Mir-184.PRE.result jobid: 194 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-184.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-184.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-873.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-873.PRE.gff, analyses/output/Amil-MirMachine/Mir-873.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-873.PRE.unfiltered jobid: 975 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-873.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-873.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-873.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:51 2023] Finished job 975. 404 of 2231 steps (18%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-873.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-873.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-873.PRE.filtered.gff jobid: 1602 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-873.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-873.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-873.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-873.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-873.PRE.filtered.fasta jobid: 2161 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-873.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-873.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-873.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:51 2023] Finished job 2161. 405 of 2231 steps (18%) done Select jobs to execute... [Fri Nov 3 10:27:51 2023] Finished job 734. 406 of 2231 steps (18%) done [Fri Nov 3 10:27:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-506.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-506.PRE.gff, analyses/output/Amil-MirMachine/Mir-506.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-506.PRE.unfiltered jobid: 733 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-506.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-506.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-506.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2061.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2061.PRE.result jobid: 316 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2061.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2061.PRE threads: 15 resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:27:51 2023] Finished job 733. 407 of 2231 steps (18%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-506.PRE.ext.gff. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-506.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-506.PRE.filtered.gff jobid: 1481 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-506.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-506.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-506.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-506.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-506.PRE.filtered.fasta jobid: 2040 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-506.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-506.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-506.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:51 2023] Finished job 1602. 408 of 2231 steps (18%) done Select jobs to execute... [Fri Nov 3 10:27:52 2023] Finished job 2040. 409 of 2231 steps (18%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:52 2023] Finished job 1481. 410 of 2231 steps (18%) done [Fri Nov 3 10:27:54 2023] Finished job 316. 411 of 2231 steps (18%) done [Fri Nov 3 10:27:54 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-249.PRE.CM output: analyses/output/Amil-MirMachine/Mir-249.PRE.result jobid: 390 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-249.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-249.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:54 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2061.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2061.PRE.gff, analyses/output/Amil-MirMachine/Mir-2061.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2061.PRE.unfiltered jobid: 315 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2061.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2061.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2061.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:55 2023] Finished job 315. 412 of 2231 steps (18%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2061.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:27:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2061.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2061.PRE.filtered.fasta jobid: 1831 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2061.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2061.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2061.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2061.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2061.PRE.filtered.gff jobid: 1272 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2061.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2061.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2061.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:55 2023] Finished job 1831. 413 of 2231 steps (19%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:55 2023] Finished job 194. 414 of 2231 steps (19%) done [Fri Nov 3 10:27:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-184.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-184.PRE.gff, analyses/output/Amil-MirMachine/Mir-184.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-184.PRE.unfiltered jobid: 193 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-184.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-184.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-184.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4542.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4542.PRE.result jobid: 616 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4542.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4542.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:27:55 2023] Finished job 1272. 415 of 2231 steps (19%) done Select jobs to execute... [Fri Nov 3 10:27:55 2023] Finished job 193. 416 of 2231 steps (19%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-184.PRE.ext.gff. [Fri Nov 3 10:27:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-184.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-184.PRE.filtered.gff jobid: 1211 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-184.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-184.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-184.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-184.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-184.PRE.filtered.fasta jobid: 1770 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-184.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-184.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-184.PRE resources: tmpdir=/tmp [Fri Nov 3 10:27:55 2023] Finished job 1770. 417 of 2231 steps (19%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:27:55 2023] Finished job 1211. 418 of 2231 steps (19%) done [Fri Nov 3 10:28:00 2023] Finished job 616. 419 of 2231 steps (19%) done [Fri Nov 3 10:28:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4542.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4542.PRE.gff, analyses/output/Amil-MirMachine/Mir-4542.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4542.PRE.unfiltered jobid: 615 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4542.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4542.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7251.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7251.PRE.result jobid: 856 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7251.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7251.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:01 2023] Finished job 615. 420 of 2231 steps (19%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4542.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4542.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4542.PRE.filtered.gff jobid: 1422 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4542.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4542.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4542.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4542.PRE.filtered.fasta jobid: 1981 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4542.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4542.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:01 2023] Finished job 1981. 421 of 2231 steps (19%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:01 2023] Finished job 1422. 422 of 2231 steps (19%) done [Fri Nov 3 10:28:01 2023] Finished job 390. 423 of 2231 steps (19%) done [Fri Nov 3 10:28:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-249.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-249.PRE.gff, analyses/output/Amil-MirMachine/Mir-249.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-249.PRE.unfiltered jobid: 389 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-249.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-249.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-249.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-146.PRE.CM output: analyses/output/Amil-MirMachine/Mir-146.PRE.result jobid: 136 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-146.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-146.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:01 2023] Finished job 389. 424 of 2231 steps (19%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-249.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-249.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-249.PRE.filtered.gff jobid: 1309 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-249.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-249.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-249.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-249.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-249.PRE.filtered.fasta jobid: 1868 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-249.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-249.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-249.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:02 2023] Finished job 1868. 425 of 2231 steps (19%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:02 2023] Finished job 1309. 426 of 2231 steps (19%) done [Fri Nov 3 10:28:04 2023] Finished job 856. 427 of 2231 steps (19%) done [Fri Nov 3 10:28:05 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7251.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7251.PRE.gff, analyses/output/Amil-MirMachine/Mir-7251.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7251.PRE.unfiltered jobid: 855 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7251.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7251.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7251.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:05 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-973.PRE.CM output: analyses/output/Amil-MirMachine/Mir-973.PRE.result jobid: 1078 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-973.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-973.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:05 2023] Finished job 855. 428 of 2231 steps (19%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7251.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:05 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7251.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7251.PRE.filtered.gff jobid: 1542 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7251.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7251.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7251.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:05 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7251.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7251.PRE.filtered.fasta jobid: 2101 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7251.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7251.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7251.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:05 2023] Finished job 2101. 429 of 2231 steps (19%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:05 2023] Finished job 1542. 430 of 2231 steps (19%) done [Fri Nov 3 10:28:10 2023] Finished job 136. 431 of 2231 steps (19%) done [Fri Nov 3 10:28:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-146.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-146.PRE.gff, analyses/output/Amil-MirMachine/Mir-146.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-146.PRE.unfiltered jobid: 135 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-146.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-146.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-146.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1842.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1842.PRE.result jobid: 196 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1842.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1842.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:10 2023] Finished job 135. 432 of 2231 steps (19%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-146.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-146.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-146.PRE.filtered.gff jobid: 1182 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-146.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-146.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-146.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-146.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-146.PRE.filtered.fasta jobid: 1741 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-146.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-146.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-146.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:10 2023] Finished job 1741. 433 of 2231 steps (19%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:11 2023] Finished job 1182. 434 of 2231 steps (19%) done [Fri Nov 3 10:28:14 2023] Finished job 196. 435 of 2231 steps (19%) done [Fri Nov 3 10:28:14 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1842.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1842.PRE.gff, analyses/output/Amil-MirMachine/Mir-1842.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1842.PRE.unfiltered jobid: 195 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1842.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1842.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1842.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:14 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7376.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7376.PRE.result jobid: 916 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7376.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7376.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:14 2023] Finished job 195. 436 of 2231 steps (20%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1842.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1842.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1842.PRE.filtered.fasta jobid: 1771 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1842.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1842.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1842.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1842.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1842.PRE.filtered.gff jobid: 1212 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1842.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1842.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1842.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:14 2023] Finished job 1771. 437 of 2231 steps (20%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:14 2023] Finished job 1212. 438 of 2231 steps (20%) done [Fri Nov 3 10:28:23 2023] Finished job 916. 439 of 2231 steps (20%) done [Fri Nov 3 10:28:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7376.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7376.PRE.gff, analyses/output/Amil-MirMachine/Mir-7376.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7376.PRE.unfiltered jobid: 915 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7376.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7376.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7376.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-128.PRE.CM output: analyses/output/Amil-MirMachine/Mir-128.PRE.result jobid: 76 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-128.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-128.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:23 2023] Finished job 915. 440 of 2231 steps (20%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7376.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7376.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7376.PRE.filtered.fasta jobid: 2131 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7376.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7376.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7376.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7376.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7376.PRE.filtered.gff jobid: 1572 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7376.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7376.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7376.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:23 2023] Finished job 2131. 441 of 2231 steps (20%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:24 2023] Finished job 1572. 442 of 2231 steps (20%) done [Fri Nov 3 10:28:28 2023] Finished job 1078. 443 of 2231 steps (20%) done [Fri Nov 3 10:28:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-491.PRE.CM output: analyses/output/Amil-MirMachine/Mir-491.PRE.result jobid: 718 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-491.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-491.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-973.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-973.PRE.gff, analyses/output/Amil-MirMachine/Mir-973.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-973.PRE.unfiltered jobid: 1077 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-973.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-973.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-973.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:28 2023] Finished job 1077. 444 of 2231 steps (20%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-973.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-973.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-973.PRE.filtered.gff jobid: 1653 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-973.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-973.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-973.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-973.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-973.PRE.filtered.fasta jobid: 2212 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-973.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-973.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-973.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:28 2023] Finished job 2212. 445 of 2231 steps (20%) done Select jobs to execute... [Fri Nov 3 10:28:28 2023] Finished job 76. 446 of 2231 steps (20%) done [Fri Nov 3 10:28:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-128.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-128.PRE.gff, analyses/output/Amil-MirMachine/Mir-128.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-128.PRE.unfiltered jobid: 75 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-128.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-128.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-128.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-238.PRE.CM output: analyses/output/Amil-MirMachine/Mir-238.PRE.result jobid: 376 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-238.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-238.PRE threads: 15 resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:28:28 2023] Finished job 75. 447 of 2231 steps (20%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-128.PRE.ext.gff. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-128.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-128.PRE.filtered.fasta jobid: 1711 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-128.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-128.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-128.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-128.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-128.PRE.filtered.gff jobid: 1152 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-128.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-128.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-128.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:28 2023] Finished job 1653. 448 of 2231 steps (20%) done Select jobs to execute... [Fri Nov 3 10:28:28 2023] Finished job 1711. 449 of 2231 steps (20%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:29 2023] Finished job 1152. 450 of 2231 steps (20%) done [Fri Nov 3 10:28:31 2023] Finished job 718. 451 of 2231 steps (20%) done [Fri Nov 3 10:28:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-491.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-491.PRE.gff, analyses/output/Amil-MirMachine/Mir-491.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-491.PRE.unfiltered jobid: 717 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-491.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-491.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-491.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4543.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4543.PRE.result jobid: 618 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4543.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4543.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:31 2023] Finished job 717. 452 of 2231 steps (20%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-491.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-491.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-491.PRE.filtered.gff jobid: 1473 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-491.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-491.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-491.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-491.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-491.PRE.filtered.fasta jobid: 2032 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-491.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-491.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-491.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:31 2023] Finished job 2032. 453 of 2231 steps (20%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:32 2023] Finished job 1473. 454 of 2231 steps (20%) done [Fri Nov 3 10:28:34 2023] Finished job 376. 455 of 2231 steps (20%) done [Fri Nov 3 10:28:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-238.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-238.PRE.gff, analyses/output/Amil-MirMachine/Mir-238.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-238.PRE.unfiltered jobid: 375 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-238.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-238.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-238.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1001.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1001.PRE.result jobid: 18 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1001.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1001.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:34 2023] Finished job 375. 456 of 2231 steps (20%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-238.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-238.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-238.PRE.filtered.gff jobid: 1302 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-238.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-238.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-238.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-238.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-238.PRE.filtered.fasta jobid: 1861 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-238.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-238.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-238.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:34 2023] Finished job 1861. 457 of 2231 steps (20%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:35 2023] Finished job 1302. 458 of 2231 steps (21%) done [Fri Nov 3 10:28:37 2023] Finished job 618. 459 of 2231 steps (21%) done [Fri Nov 3 10:28:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4543.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4543.PRE.gff, analyses/output/Amil-MirMachine/Mir-4543.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4543.PRE.unfiltered jobid: 617 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4543.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4543.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4543.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7254.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7254.PRE.result jobid: 858 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7254.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7254.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:38 2023] Finished job 617. 460 of 2231 steps (21%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4543.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4543.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4543.PRE.filtered.gff jobid: 1423 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4543.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4543.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4543.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4543.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4543.PRE.filtered.fasta jobid: 1982 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4543.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4543.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4543.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:38 2023] Finished job 1982. 461 of 2231 steps (21%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:38 2023] Finished job 1423. 462 of 2231 steps (21%) done [Fri Nov 3 10:28:40 2023] Finished job 18. 463 of 2231 steps (21%) done [Fri Nov 3 10:28:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1001.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1001.PRE.gff, analyses/output/Amil-MirMachine/Mir-1001.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1001.PRE.unfiltered jobid: 17 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1001.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1001.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1001.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7377.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7377.PRE.result jobid: 918 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7377.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7377.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:40 2023] Finished job 17. 464 of 2231 steps (21%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1001.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1001.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1001.PRE.filtered.fasta jobid: 1682 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1001.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1001.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1001.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1001.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1001.PRE.filtered.gff jobid: 1123 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1001.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1001.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1001.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:40 2023] Finished job 1682. 465 of 2231 steps (21%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:40 2023] Finished job 1123. 466 of 2231 steps (21%) done [Fri Nov 3 10:28:42 2023] Finished job 858. 467 of 2231 steps (21%) done [Fri Nov 3 10:28:42 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-5305.PRE.CM output: analyses/output/Amil-MirMachine/Mir-5305.PRE.result jobid: 740 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5305.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-5305.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:42 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7254.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7254.PRE.gff, analyses/output/Amil-MirMachine/Mir-7254.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7254.PRE.unfiltered jobid: 857 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7254.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7254.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7254.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:42 2023] Finished job 857. 468 of 2231 steps (21%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7254.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7254.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7254.PRE.filtered.gff jobid: 1543 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7254.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7254.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7254.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7254.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7254.PRE.filtered.fasta jobid: 2102 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7254.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7254.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7254.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:42 2023] Finished job 2102. 469 of 2231 steps (21%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:42 2023] Finished job 1543. 470 of 2231 steps (21%) done [Fri Nov 3 10:28:44 2023] Finished job 918. 471 of 2231 steps (21%) done [Fri Nov 3 10:28:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7377.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7377.PRE.gff, analyses/output/Amil-MirMachine/Mir-7377.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7377.PRE.unfiltered jobid: 917 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7377.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7377.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7377.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1467.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1467.PRE.result jobid: 138 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1467.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1467.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:44 2023] Finished job 917. 472 of 2231 steps (21%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7377.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7377.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7377.PRE.filtered.fasta jobid: 2132 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7377.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7377.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7377.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7377.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7377.PRE.filtered.gff jobid: 1573 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7377.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7377.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7377.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:44 2023] Finished job 2132. 473 of 2231 steps (21%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:44 2023] Finished job 1573. 474 of 2231 steps (21%) done [Fri Nov 3 10:28:49 2023] Finished job 740. 475 of 2231 steps (21%) done [Fri Nov 3 10:28:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3059.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3059.PRE.result jobid: 478 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3059.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3059.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-5305.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-5305.PRE.gff, analyses/output/Amil-MirMachine/Mir-5305.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-5305.PRE.unfiltered jobid: 739 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5305.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-5305.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-5305.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:49 2023] Finished job 739. 476 of 2231 steps (21%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-5305.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-5305.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-5305.PRE.filtered.fasta jobid: 2043 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5305.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-5305.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-5305.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-5305.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-5305.PRE.filtered.gff jobid: 1484 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5305.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-5305.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-5305.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:49 2023] Finished job 2043. 477 of 2231 steps (21%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:49 2023] Finished job 1484. 478 of 2231 steps (21%) done [Fri Nov 3 10:28:50 2023] Finished job 138. 479 of 2231 steps (21%) done [Fri Nov 3 10:28:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1467.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1467.PRE.gff, analyses/output/Amil-MirMachine/Mir-1467.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1467.PRE.unfiltered jobid: 137 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1467.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1467.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1467.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2387.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2387.PRE.result jobid: 378 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2387.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2387.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:50 2023] Finished job 137. 480 of 2231 steps (22%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1467.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1467.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1467.PRE.filtered.gff jobid: 1183 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1467.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1467.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1467.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1467.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1467.PRE.filtered.fasta jobid: 1742 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1467.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1467.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1467.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:50 2023] Finished job 1742. 481 of 2231 steps (22%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:50 2023] Finished job 1183. 482 of 2231 steps (22%) done [Fri Nov 3 10:28:52 2023] Finished job 478. 483 of 2231 steps (22%) done [Fri Nov 3 10:28:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3059.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3059.PRE.gff, analyses/output/Amil-MirMachine/Mir-3059.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3059.PRE.unfiltered jobid: 477 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3059.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-3059.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3059.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-874.PRE.CM output: analyses/output/Amil-MirMachine/Mir-874.PRE.result jobid: 978 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-874.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-874.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:52 2023] Finished job 477. 484 of 2231 steps (22%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3059.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3059.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3059.PRE.filtered.gff jobid: 1353 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3059.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3059.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3059.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3059.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3059.PRE.filtered.fasta jobid: 1912 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3059.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3059.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3059.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:53 2023] Finished job 1912. 485 of 2231 steps (22%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:53 2023] Finished job 1353. 486 of 2231 steps (22%) done [Fri Nov 3 10:28:53 2023] Finished job 378. 487 of 2231 steps (22%) done [Fri Nov 3 10:28:53 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2387.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2387.PRE.gff, analyses/output/Amil-MirMachine/Mir-2387.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2387.PRE.unfiltered jobid: 377 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2387.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2387.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2387.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:53 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-185.PRE.CM output: analyses/output/Amil-MirMachine/Mir-185.PRE.result jobid: 198 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-185.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-185.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:53 2023] Finished job 377. 488 of 2231 steps (22%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2387.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2387.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2387.PRE.filtered.gff jobid: 1303 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2387.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2387.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2387.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2387.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2387.PRE.filtered.fasta jobid: 1862 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2387.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2387.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2387.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:53 2023] Finished job 1862. 489 of 2231 steps (22%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:54 2023] Finished job 1303. 490 of 2231 steps (22%) done [Fri Nov 3 10:28:55 2023] Finished job 978. 491 of 2231 steps (22%) done [Fri Nov 3 10:28:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-976.PRE.CM output: analyses/output/Amil-MirMachine/Mir-976.PRE.result jobid: 1084 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-976.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-976.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-874.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-874.PRE.gff, analyses/output/Amil-MirMachine/Mir-874.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-874.PRE.unfiltered jobid: 977 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-874.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-874.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-874.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:55 2023] Finished job 977. 492 of 2231 steps (22%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-874.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-874.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-874.PRE.filtered.gff jobid: 1603 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-874.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-874.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-874.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-874.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-874.PRE.filtered.fasta jobid: 2162 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-874.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-874.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-874.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:55 2023] Finished job 2162. 493 of 2231 steps (22%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:56 2023] Finished job 1603. 494 of 2231 steps (22%) done [Fri Nov 3 10:28:56 2023] Finished job 198. 495 of 2231 steps (22%) done [Fri Nov 3 10:28:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-185.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-185.PRE.gff, analyses/output/Amil-MirMachine/Mir-185.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-185.PRE.unfiltered jobid: 197 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-185.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-185.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-185.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-52.PRE.CM output: analyses/output/Amil-MirMachine/Mir-52.PRE.result jobid: 738 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-52.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-52.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:28:56 2023] Finished job 197. 496 of 2231 steps (22%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-185.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:28:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-185.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-185.PRE.filtered.fasta jobid: 1772 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-185.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-185.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-185.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-185.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-185.PRE.filtered.gff jobid: 1213 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-185.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-185.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-185.PRE resources: tmpdir=/tmp [Fri Nov 3 10:28:56 2023] Finished job 1772. 497 of 2231 steps (22%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:28:57 2023] Finished job 1213. 498 of 2231 steps (22%) done [Fri Nov 3 10:29:02 2023] Finished job 1084. 499 of 2231 steps (22%) done [Fri Nov 3 10:29:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-976.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-976.PRE.gff, analyses/output/Amil-MirMachine/Mir-976.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-976.PRE.unfiltered jobid: 1083 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-976.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-976.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-976.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2062.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2062.PRE.result jobid: 318 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2062.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2062.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:02 2023] Finished job 1083. 500 of 2231 steps (22%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-976.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-976.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-976.PRE.filtered.fasta jobid: 2215 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-976.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-976.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-976.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-976.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-976.PRE.filtered.gff jobid: 1656 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-976.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-976.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-976.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:02 2023] Finished job 2215. 501 of 2231 steps (22%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:03 2023] Finished job 1656. 502 of 2231 steps (23%) done [Fri Nov 3 10:29:03 2023] Finished job 738. 503 of 2231 steps (23%) done [Fri Nov 3 10:29:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1994.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1994.PRE.result jobid: 248 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1994.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1994.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-52.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-52.PRE.gff, analyses/output/Amil-MirMachine/Mir-52.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-52.PRE.unfiltered jobid: 737 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-52.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-52.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-52.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:03 2023] Finished job 737. 504 of 2231 steps (23%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-52.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-52.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-52.PRE.filtered.gff jobid: 1483 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-52.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-52.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-52.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-52.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-52.PRE.filtered.fasta jobid: 2042 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-52.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-52.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-52.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:03 2023] Finished job 2042. 505 of 2231 steps (23%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:03 2023] Finished job 1483. 506 of 2231 steps (23%) done [Fri Nov 3 10:29:06 2023] Finished job 318. 507 of 2231 steps (23%) done [Fri Nov 3 10:29:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3085.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3085.PRE.result jobid: 488 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3085.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3085.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2062.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2062.PRE.gff, analyses/output/Amil-MirMachine/Mir-2062.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2062.PRE.unfiltered jobid: 317 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2062.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2062.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2062.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:06 2023] Finished job 317. 508 of 2231 steps (23%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2062.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2062.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2062.PRE.filtered.fasta jobid: 1832 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2062.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2062.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2062.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2062.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2062.PRE.filtered.gff jobid: 1273 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2062.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2062.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2062.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:06 2023] Finished job 1832. 509 of 2231 steps (23%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:07 2023] Finished job 1273. 510 of 2231 steps (23%) done [Fri Nov 3 10:29:08 2023] Finished job 248. 511 of 2231 steps (23%) done [Fri Nov 3 10:29:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1994.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1994.PRE.gff, analyses/output/Amil-MirMachine/Mir-1994.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1994.PRE.unfiltered jobid: 247 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1994.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1994.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1994.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-129.PRE.CM output: analyses/output/Amil-MirMachine/Mir-129.PRE.result jobid: 78 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-129.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-129.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:08 2023] Finished job 247. 512 of 2231 steps (23%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1994.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1994.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1994.PRE.filtered.gff jobid: 1238 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1994.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1994.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1994.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1994.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1994.PRE.filtered.fasta jobid: 1797 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1994.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1994.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1994.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:09 2023] Finished job 1797. 513 of 2231 steps (23%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:09 2023] Finished job 1238. 514 of 2231 steps (23%) done [Fri Nov 3 10:29:11 2023] Finished job 488. 515 of 2231 steps (23%) done [Fri Nov 3 10:29:11 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3085.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3085.PRE.gff, analyses/output/Amil-MirMachine/Mir-3085.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3085.PRE.unfiltered jobid: 487 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3085.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3085.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3085.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:11 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2689.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2689.PRE.result jobid: 418 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2689.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2689.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:11 2023] Finished job 487. 516 of 2231 steps (23%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3085.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3085.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3085.PRE.filtered.gff jobid: 1358 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3085.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3085.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3085.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3085.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3085.PRE.filtered.fasta jobid: 1917 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3085.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3085.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3085.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:11 2023] Finished job 1917. 517 of 2231 steps (23%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:11 2023] Finished job 1358. 518 of 2231 steps (23%) done [Fri Nov 3 10:29:14 2023] Finished job 418. 519 of 2231 steps (23%) done [Fri Nov 3 10:29:14 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1296.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1296.PRE.result jobid: 80 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1296.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1296.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:14 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2689.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2689.PRE.gff, analyses/output/Amil-MirMachine/Mir-2689.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2689.PRE.unfiltered jobid: 417 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2689.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2689.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2689.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:14 2023] Finished job 417. 520 of 2231 steps (23%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2689.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2689.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2689.PRE.filtered.fasta jobid: 1882 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2689.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2689.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2689.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2689.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2689.PRE.filtered.gff jobid: 1323 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2689.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2689.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2689.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:14 2023] Finished job 1882. 521 of 2231 steps (23%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:15 2023] Finished job 1323. 522 of 2231 steps (23%) done [Fri Nov 3 10:29:15 2023] Finished job 78. 523 of 2231 steps (23%) done [Fri Nov 3 10:29:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1003.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1003.PRE.result jobid: 20 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1003.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1003.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-129.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-129.PRE.gff, analyses/output/Amil-MirMachine/Mir-129.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-129.PRE.unfiltered jobid: 77 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-129.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-129.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-129.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:15 2023] Finished job 77. 524 of 2231 steps (23%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-129.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-129.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-129.PRE.filtered.fasta jobid: 1712 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-129.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-129.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-129.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-129.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-129.PRE.filtered.gff jobid: 1153 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-129.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-129.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-129.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:15 2023] Finished job 1712. 525 of 2231 steps (24%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:16 2023] Finished job 1153. 526 of 2231 steps (24%) done [Fri Nov 3 10:29:18 2023] Finished job 80. 527 of 2231 steps (24%) done [Fri Nov 3 10:29:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2068.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2068.PRE.result jobid: 320 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2068.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2068.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1296.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1296.PRE.gff, analyses/output/Amil-MirMachine/Mir-1296.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1296.PRE.unfiltered jobid: 79 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1296.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1296.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1296.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:18 2023] Finished job 79. 528 of 2231 steps (24%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1296.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:18 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1296.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1296.PRE.filtered.fasta jobid: 1713 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1296.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1296.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1296.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:18 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1296.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1296.PRE.filtered.gff jobid: 1154 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1296.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1296.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1296.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:18 2023] Finished job 1713. 529 of 2231 steps (24%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:19 2023] Finished job 1154. 530 of 2231 steps (24%) done [Fri Nov 3 10:29:20 2023] Finished job 20. 531 of 2231 steps (24%) done [Fri Nov 3 10:29:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-431.PRE.CM output: analyses/output/Amil-MirMachine/Mir-431.PRE.result jobid: 598 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-431.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-431.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1003.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1003.PRE.gff, analyses/output/Amil-MirMachine/Mir-1003.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1003.PRE.unfiltered jobid: 19 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1003.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1003.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1003.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:20 2023] Finished job 19. 532 of 2231 steps (24%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1003.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1003.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1003.PRE.filtered.fasta jobid: 1683 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1003.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1003.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1003.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1003.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1003.PRE.filtered.gff jobid: 1124 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1003.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1003.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1003.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:20 2023] Finished job 1683. 533 of 2231 steps (24%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:20 2023] Finished job 1124. 534 of 2231 steps (24%) done [Fri Nov 3 10:29:22 2023] Finished job 320. 535 of 2231 steps (24%) done [Fri Nov 3 10:29:22 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-24.PRE.CM output: analyses/output/Amil-MirMachine/Mir-24.PRE.result jobid: 380 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-24.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-24.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:22 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2068.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2068.PRE.gff, analyses/output/Amil-MirMachine/Mir-2068.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2068.PRE.unfiltered jobid: 319 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2068.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2068.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2068.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:22 2023] Finished job 319. 536 of 2231 steps (24%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2068.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:22 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2068.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2068.PRE.filtered.fasta jobid: 1833 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2068.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2068.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2068.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:22 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2068.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2068.PRE.filtered.gff jobid: 1274 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2068.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2068.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2068.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:22 2023] Finished job 1833. 537 of 2231 steps (24%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:22 2023] Finished job 1274. 538 of 2231 steps (24%) done [Fri Nov 3 10:29:22 2023] Finished job 598. 539 of 2231 steps (24%) done [Fri Nov 3 10:29:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-431.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-431.PRE.gff, analyses/output/Amil-MirMachine/Mir-431.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-431.PRE.unfiltered jobid: 597 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-431.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-431.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-431.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2021.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2021.PRE.result jobid: 298 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2021.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2021.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:23 2023] Finished job 597. 540 of 2231 steps (24%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-431.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-431.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-431.PRE.filtered.gff jobid: 1413 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-431.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-431.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-431.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-431.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-431.PRE.filtered.fasta jobid: 1972 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-431.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-431.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-431.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:23 2023] Finished job 1972. 541 of 2231 steps (24%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:23 2023] Finished job 1413. 542 of 2231 steps (24%) done [Fri Nov 3 10:29:27 2023] Finished job 380. 543 of 2231 steps (24%) done [Fri Nov 3 10:29:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4544.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4544.PRE.result jobid: 620 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4544.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4544.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-24.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-24.PRE.gff, analyses/output/Amil-MirMachine/Mir-24.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-24.PRE.unfiltered jobid: 379 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-24.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-24.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-24.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:27 2023] Finished job 379. 544 of 2231 steps (24%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-24.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-24.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-24.PRE.filtered.fasta jobid: 1863 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-24.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-24.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-24.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-24.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-24.PRE.filtered.gff jobid: 1304 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-24.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-24.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-24.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:27 2023] Finished job 1863. 545 of 2231 steps (24%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:27 2023] Finished job 1304. 546 of 2231 steps (24%) done [Fri Nov 3 10:29:27 2023] Finished job 298. 547 of 2231 steps (25%) done [Fri Nov 3 10:29:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-726.PRE.CM output: analyses/output/Amil-MirMachine/Mir-726.PRE.result jobid: 860 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-726.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-726.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2021.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2021.PRE.gff, analyses/output/Amil-MirMachine/Mir-2021.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2021.PRE.unfiltered jobid: 297 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2021.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2021.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2021.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:28 2023] Finished job 297. 548 of 2231 steps (25%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2021.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2021.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2021.PRE.filtered.fasta jobid: 1822 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2021.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2021.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2021.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2021.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2021.PRE.filtered.gff jobid: 1263 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2021.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2021.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2021.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:28 2023] Finished job 1822. 549 of 2231 steps (25%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:28 2023] Finished job 1263. 550 of 2231 steps (25%) done [Fri Nov 3 10:29:31 2023] Finished job 620. 551 of 2231 steps (25%) done [Fri Nov 3 10:29:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-147.PRE.CM output: analyses/output/Amil-MirMachine/Mir-147.PRE.result jobid: 140 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-147.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-147.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4544.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4544.PRE.gff, analyses/output/Amil-MirMachine/Mir-4544.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4544.PRE.unfiltered jobid: 619 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4544.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4544.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4544.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:31 2023] Finished job 619. 552 of 2231 steps (25%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4544.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4544.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4544.PRE.filtered.fasta jobid: 1983 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4544.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4544.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4544.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4544.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4544.PRE.filtered.gff jobid: 1424 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4544.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4544.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4544.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:31 2023] Finished job 1983. 553 of 2231 steps (25%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:31 2023] Finished job 1424. 554 of 2231 steps (25%) done [Fri Nov 3 10:29:33 2023] Finished job 860. 555 of 2231 steps (25%) done [Fri Nov 3 10:29:33 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7148.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7148.PRE.result jobid: 838 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7148.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7148.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:33 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-726.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-726.PRE.gff, analyses/output/Amil-MirMachine/Mir-726.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-726.PRE.unfiltered jobid: 859 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-726.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-726.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-726.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:33 2023] Finished job 859. 556 of 2231 steps (25%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-726.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-726.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-726.PRE.filtered.fasta jobid: 2103 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-726.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-726.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-726.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-726.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-726.PRE.filtered.gff jobid: 1544 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-726.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-726.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-726.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:34 2023] Finished job 2103. 557 of 2231 steps (25%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:34 2023] Finished job 1544. 558 of 2231 steps (25%) done [Fri Nov 3 10:29:37 2023] Finished job 140. 559 of 2231 steps (25%) done [Fri Nov 3 10:29:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7378.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7378.PRE.result jobid: 920 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7378.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7378.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-147.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-147.PRE.gff, analyses/output/Amil-MirMachine/Mir-147.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-147.PRE.unfiltered jobid: 139 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-147.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-147.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-147.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:37 2023] Finished job 139. 560 of 2231 steps (25%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-147.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-147.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-147.PRE.filtered.fasta jobid: 1743 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-147.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-147.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-147.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-147.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-147.PRE.filtered.gff jobid: 1184 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-147.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-147.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-147.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:37 2023] Finished job 1743. 561 of 2231 steps (25%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:37 2023] Finished job 1184. 562 of 2231 steps (25%) done [Fri Nov 3 10:29:38 2023] Finished job 838. 563 of 2231 steps (25%) done [Fri Nov 3 10:29:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-875.PRE.CM output: analyses/output/Amil-MirMachine/Mir-875.PRE.result jobid: 980 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-875.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-875.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7148.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7148.PRE.gff, analyses/output/Amil-MirMachine/Mir-7148.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7148.PRE.unfiltered jobid: 837 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7148.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7148.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7148.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:38 2023] Finished job 837. 564 of 2231 steps (25%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7148.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7148.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7148.PRE.filtered.gff jobid: 1533 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7148.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7148.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7148.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7148.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7148.PRE.filtered.fasta jobid: 2092 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7148.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7148.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7148.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:38 2023] Finished job 2092. 565 of 2231 steps (25%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:39 2023] Finished job 1533. 566 of 2231 steps (25%) done [Fri Nov 3 10:29:40 2023] Finished job 920. 567 of 2231 steps (25%) done [Fri Nov 3 10:29:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-876.PRE.CM output: analyses/output/Amil-MirMachine/Mir-876.PRE.result jobid: 982 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-876.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-876.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7378.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7378.PRE.gff, analyses/output/Amil-MirMachine/Mir-7378.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7378.PRE.unfiltered jobid: 919 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7378.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7378.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7378.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:40 2023] Finished job 919. 568 of 2231 steps (25%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7378.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7378.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7378.PRE.filtered.fasta jobid: 2133 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7378.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7378.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7378.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7378.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7378.PRE.filtered.gff jobid: 1574 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7378.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7378.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7378.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:41 2023] Finished job 2133. 569 of 2231 steps (26%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:41 2023] Finished job 1574. 570 of 2231 steps (26%) done [Fri Nov 3 10:29:44 2023] Finished job 980. 571 of 2231 steps (26%) done [Fri Nov 3 10:29:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-54.PRE.CM output: analyses/output/Amil-MirMachine/Mir-54.PRE.result jobid: 742 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-54.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-54.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-875.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-875.PRE.gff, analyses/output/Amil-MirMachine/Mir-875.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-875.PRE.unfiltered jobid: 979 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-875.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-875.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-875.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:45 2023] Finished job 979. 572 of 2231 steps (26%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-875.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-875.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-875.PRE.filtered.fasta jobid: 2163 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-875.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-875.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-875.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-875.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-875.PRE.filtered.gff jobid: 1604 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-875.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-875.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-875.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:45 2023] Finished job 2163. 573 of 2231 steps (26%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:45 2023] Finished job 1604. 574 of 2231 steps (26%) done [Fri Nov 3 10:29:45 2023] Finished job 982. 575 of 2231 steps (26%) done [Fri Nov 3 10:29:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-876.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-876.PRE.gff, analyses/output/Amil-MirMachine/Mir-876.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-876.PRE.unfiltered jobid: 981 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-876.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-876.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-876.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1006.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1006.PRE.result jobid: 22 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1006.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1006.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:45 2023] Finished job 981. 576 of 2231 steps (26%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-876.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-876.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-876.PRE.filtered.gff jobid: 1605 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-876.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-876.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-876.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-876.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-876.PRE.filtered.fasta jobid: 2164 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-876.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-876.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-876.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:46 2023] Finished job 2164. 577 of 2231 steps (26%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:46 2023] Finished job 1605. 578 of 2231 steps (26%) done [Fri Nov 3 10:29:49 2023] Finished job 742. 579 of 2231 steps (26%) done [Fri Nov 3 10:29:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-54.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-54.PRE.gff, analyses/output/Amil-MirMachine/Mir-54.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-54.PRE.unfiltered jobid: 741 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-54.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-54.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-54.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1298.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1298.PRE.result jobid: 82 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1298.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1298.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:49 2023] Finished job 741. 580 of 2231 steps (26%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-54.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-54.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-54.PRE.filtered.gff jobid: 1485 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-54.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-54.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-54.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-54.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-54.PRE.filtered.fasta jobid: 2044 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-54.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-54.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-54.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:49 2023] Finished job 2044. 581 of 2231 steps (26%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:49 2023] Finished job 1485. 582 of 2231 steps (26%) done [Fri Nov 3 10:29:54 2023] Finished job 82. 583 of 2231 steps (26%) done [Fri Nov 3 10:29:54 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1298.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1298.PRE.gff, analyses/output/Amil-MirMachine/Mir-1298.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1298.PRE.unfiltered jobid: 81 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1298.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1298.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1298.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:54 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-242.PRE.CM output: analyses/output/Amil-MirMachine/Mir-242.PRE.result jobid: 382 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-242.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-242.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:54 2023] Finished job 81. 584 of 2231 steps (26%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1298.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:54 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1298.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1298.PRE.filtered.fasta jobid: 1714 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1298.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1298.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1298.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:54 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1298.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1298.PRE.filtered.gff jobid: 1155 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1298.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1298.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1298.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:54 2023] Finished job 1714. 585 of 2231 steps (26%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:29:55 2023] Finished job 22. 586 of 2231 steps (26%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-186.PRE.CM output: analyses/output/Amil-MirMachine/Mir-186.PRE.result jobid: 200 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-186.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-186.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1006.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1006.PRE.gff, analyses/output/Amil-MirMachine/Mir-1006.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1006.PRE.unfiltered jobid: 21 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1006.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1006.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1006.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:55 2023] Finished job 1155. 587 of 2231 steps (26%) done Select jobs to execute... [Fri Nov 3 10:29:55 2023] Finished job 21. 588 of 2231 steps (26%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1006.PRE.ext.gff. [Fri Nov 3 10:29:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1006.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1006.PRE.filtered.gff jobid: 1125 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1006.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1006.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1006.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1006.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1006.PRE.filtered.fasta jobid: 1684 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1006.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1006.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1006.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:55 2023] Finished job 1684. 589 of 2231 steps (26%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:55 2023] Finished job 1125. 590 of 2231 steps (26%) done [Fri Nov 3 10:29:58 2023] Finished job 382. 591 of 2231 steps (26%) done [Fri Nov 3 10:29:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-242.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-242.PRE.gff, analyses/output/Amil-MirMachine/Mir-242.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-242.PRE.unfiltered jobid: 381 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-242.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-242.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-242.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2070.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2070.PRE.result jobid: 322 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2070.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2070.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:29:58 2023] Finished job 381. 592 of 2231 steps (27%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-242.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:29:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-242.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-242.PRE.filtered.gff jobid: 1305 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-242.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-242.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-242.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-242.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-242.PRE.filtered.fasta jobid: 1864 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-242.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-242.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-242.PRE resources: tmpdir=/tmp [Fri Nov 3 10:29:58 2023] Finished job 1864. 593 of 2231 steps (27%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:29:59 2023] Finished job 1305. 594 of 2231 steps (27%) done [Fri Nov 3 10:30:04 2023] Finished job 322. 595 of 2231 steps (27%) done [Fri Nov 3 10:30:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2070.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2070.PRE.gff, analyses/output/Amil-MirMachine/Mir-2070.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2070.PRE.unfiltered jobid: 321 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2070.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2070.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2070.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-339.PRE.CM output: analyses/output/Amil-MirMachine/Mir-339.PRE.result jobid: 538 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-339.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-339.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:04 2023] Finished job 321. 596 of 2231 steps (27%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2070.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2070.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2070.PRE.filtered.fasta jobid: 1834 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2070.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2070.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2070.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2070.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2070.PRE.filtered.gff jobid: 1275 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2070.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2070.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2070.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:04 2023] Finished job 1834. 597 of 2231 steps (27%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:05 2023] Finished job 1275. 598 of 2231 steps (27%) done [Fri Nov 3 10:30:08 2023] Finished job 538. 599 of 2231 steps (27%) done [Fri Nov 3 10:30:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4545.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4545.PRE.result jobid: 622 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4545.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4545.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-339.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-339.PRE.gff, analyses/output/Amil-MirMachine/Mir-339.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-339.PRE.unfiltered jobid: 537 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-339.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-339.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-339.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:08 2023] Finished job 537. 600 of 2231 steps (27%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-339.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-339.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-339.PRE.filtered.fasta jobid: 1942 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-339.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-339.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-339.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-339.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-339.PRE.filtered.gff jobid: 1383 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-339.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-339.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-339.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:08 2023] Finished job 1942. 601 of 2231 steps (27%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:09 2023] Finished job 1383. 602 of 2231 steps (27%) done [Fri Nov 3 10:30:10 2023] Finished job 200. 603 of 2231 steps (27%) done [Fri Nov 3 10:30:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-972.PRE.CM output: analyses/output/Amil-MirMachine/Mir-972.PRE.result jobid: 1076 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-972.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-972.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-186.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-186.PRE.gff, analyses/output/Amil-MirMachine/Mir-186.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-186.PRE.unfiltered jobid: 199 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-186.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-186.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-186.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:10 2023] Finished job 199. 604 of 2231 steps (27%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-186.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-186.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-186.PRE.filtered.fasta jobid: 1773 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-186.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-186.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-186.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-186.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-186.PRE.filtered.gff jobid: 1214 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-186.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-186.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-186.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:10 2023] Finished job 1773. 605 of 2231 steps (27%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:10 2023] Finished job 1214. 606 of 2231 steps (27%) done [Fri Nov 3 10:30:13 2023] Finished job 622. 607 of 2231 steps (27%) done [Fri Nov 3 10:30:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4545.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4545.PRE.gff, analyses/output/Amil-MirMachine/Mir-4545.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4545.PRE.unfiltered jobid: 621 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4545.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4545.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4545.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7262.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7262.PRE.result jobid: 862 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7262.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7262.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:13 2023] Finished job 621. 608 of 2231 steps (27%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4545.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4545.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4545.PRE.filtered.fasta jobid: 1984 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4545.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4545.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4545.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4545.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4545.PRE.filtered.gff jobid: 1425 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4545.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4545.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4545.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:13 2023] Finished job 1984. 609 of 2231 steps (27%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:14 2023] Finished job 1425. 610 of 2231 steps (27%) done [Fri Nov 3 10:30:31 2023] Finished job 862. 611 of 2231 steps (27%) done [Fri Nov 3 10:30:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7262.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7262.PRE.gff, analyses/output/Amil-MirMachine/Mir-7262.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7262.PRE.unfiltered jobid: 861 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7262.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7262.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7262.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-148.PRE.CM output: analyses/output/Amil-MirMachine/Mir-148.PRE.result jobid: 142 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-148.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-148.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:31 2023] Finished job 861. 612 of 2231 steps (27%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7262.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7262.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7262.PRE.filtered.fasta jobid: 2104 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7262.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7262.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7262.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7262.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7262.PRE.filtered.gff jobid: 1545 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7262.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7262.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7262.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:31 2023] Finished job 2104. 613 of 2231 steps (27%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:32 2023] Finished job 1545. 614 of 2231 steps (28%) done [Fri Nov 3 10:30:39 2023] Finished job 142. 615 of 2231 steps (28%) done [Fri Nov 3 10:30:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-148.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-148.PRE.gff, analyses/output/Amil-MirMachine/Mir-148.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-148.PRE.unfiltered jobid: 141 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-148.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-148.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-148.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-187.PRE.CM output: analyses/output/Amil-MirMachine/Mir-187.PRE.result jobid: 202 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-187.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-187.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:39 2023] Finished job 141. 616 of 2231 steps (28%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-148.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-148.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-148.PRE.filtered.gff jobid: 1185 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-148.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-148.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-148.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-148.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-148.PRE.filtered.fasta jobid: 1744 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-148.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-148.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-148.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:39 2023] Finished job 1744. 617 of 2231 steps (28%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:39 2023] Finished job 1185. 618 of 2231 steps (28%) done [Fri Nov 3 10:30:40 2023] Finished job 1076. 619 of 2231 steps (28%) done [Fri Nov 3 10:30:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-972.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-972.PRE.gff, analyses/output/Amil-MirMachine/Mir-972.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-972.PRE.unfiltered jobid: 1075 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-972.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-972.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-972.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2020.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2020.PRE.result jobid: 296 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2020.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2020.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:40 2023] Finished job 1075. 620 of 2231 steps (28%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-972.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-972.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-972.PRE.filtered.fasta jobid: 2211 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-972.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-972.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-972.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-972.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-972.PRE.filtered.gff jobid: 1652 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-972.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-972.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-972.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:40 2023] Finished job 2211. 621 of 2231 steps (28%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:41 2023] Finished job 1652. 622 of 2231 steps (28%) done [Fri Nov 3 10:30:43 2023] Finished job 202. 623 of 2231 steps (28%) done [Fri Nov 3 10:30:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-187.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-187.PRE.gff, analyses/output/Amil-MirMachine/Mir-187.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-187.PRE.unfiltered jobid: 201 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-187.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-187.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-187.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7379.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7379.PRE.result jobid: 922 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7379.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7379.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:43 2023] Finished job 201. 624 of 2231 steps (28%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-187.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-187.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-187.PRE.filtered.fasta jobid: 1774 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-187.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-187.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-187.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-187.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-187.PRE.filtered.gff jobid: 1215 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-187.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-187.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-187.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:43 2023] Finished job 1774. 625 of 2231 steps (28%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:43 2023] Finished job 1215. 626 of 2231 steps (28%) done [Fri Nov 3 10:30:45 2023] Finished job 296. 627 of 2231 steps (28%) done [Fri Nov 3 10:30:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2020.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2020.PRE.gff, analyses/output/Amil-MirMachine/Mir-2020.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2020.PRE.unfiltered jobid: 295 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2020.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-2020.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2020.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-455.PRE.CM output: analyses/output/Amil-MirMachine/Mir-455.PRE.result jobid: 624 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-455.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-455.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:45 2023] Finished job 295. 628 of 2231 steps (28%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2020.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2020.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2020.PRE.filtered.fasta jobid: 1821 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2020.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2020.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2020.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2020.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2020.PRE.filtered.gff jobid: 1262 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2020.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2020.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2020.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:46 2023] Finished job 1821. 629 of 2231 steps (28%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:46 2023] Finished job 1262. 630 of 2231 steps (28%) done [Fri Nov 3 10:30:50 2023] Finished job 922. 631 of 2231 steps (28%) done [Fri Nov 3 10:30:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7379.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7379.PRE.gff, analyses/output/Amil-MirMachine/Mir-7379.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7379.PRE.unfiltered jobid: 921 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7379.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7379.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7379.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-727.PRE.CM output: analyses/output/Amil-MirMachine/Mir-727.PRE.result jobid: 864 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-727.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-727.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] Finished job 921. 632 of 2231 steps (28%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7379.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7379.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7379.PRE.filtered.fasta jobid: 2134 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7379.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7379.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7379.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7379.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7379.PRE.filtered.gff jobid: 1575 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7379.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7379.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7379.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] Finished job 624. 633 of 2231 steps (28%) done Select jobs to execute... [Fri Nov 3 10:30:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-62.PRE.CM output: analyses/output/Amil-MirMachine/Mir-62.PRE.result jobid: 784 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-62.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-62.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-455.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-455.PRE.gff, analyses/output/Amil-MirMachine/Mir-455.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-455.PRE.unfiltered jobid: 623 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-455.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-455.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-455.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] Finished job 2134. 634 of 2231 steps (28%) done Select jobs to execute... [Fri Nov 3 10:30:50 2023] Finished job 623. 635 of 2231 steps (28%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-455.PRE.ext.gff. [Fri Nov 3 10:30:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-455.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-455.PRE.filtered.fasta jobid: 1985 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-455.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-455.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-455.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-455.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-455.PRE.filtered.gff jobid: 1426 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-455.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-455.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-455.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:50 2023] Finished job 1985. 636 of 2231 steps (29%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:50 2023] Finished job 1575. 637 of 2231 steps (29%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:50 2023] Finished job 1426. 638 of 2231 steps (29%) done [Fri Nov 3 10:30:54 2023] Finished job 784. 639 of 2231 steps (29%) done [Fri Nov 3 10:30:54 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-149.PRE.CM output: analyses/output/Amil-MirMachine/Mir-149.PRE.result jobid: 144 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-149.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-149.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:54 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-62.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-62.PRE.gff, analyses/output/Amil-MirMachine/Mir-62.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-62.PRE.unfiltered jobid: 783 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-62.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-62.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-62.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:54 2023] Finished job 783. 640 of 2231 steps (29%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-62.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:54 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-62.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-62.PRE.filtered.gff jobid: 1506 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-62.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-62.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-62.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:54 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-62.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-62.PRE.filtered.fasta jobid: 2065 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-62.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-62.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-62.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:54 2023] Finished job 2065. 641 of 2231 steps (29%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:55 2023] Finished job 1506. 642 of 2231 steps (29%) done [Fri Nov 3 10:30:56 2023] Finished job 864. 643 of 2231 steps (29%) done [Fri Nov 3 10:30:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-727.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-727.PRE.gff, analyses/output/Amil-MirMachine/Mir-727.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-727.PRE.unfiltered jobid: 863 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-727.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-727.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-727.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-188.PRE.CM output: analyses/output/Amil-MirMachine/Mir-188.PRE.result jobid: 204 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-188.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-188.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:56 2023] Finished job 863. 644 of 2231 steps (29%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-727.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-727.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-727.PRE.filtered.fasta jobid: 2105 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-727.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-727.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-727.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-727.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-727.PRE.filtered.gff jobid: 1546 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-727.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-727.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-727.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:56 2023] Finished job 2105. 645 of 2231 steps (29%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:56 2023] Finished job 1546. 646 of 2231 steps (29%) done [Fri Nov 3 10:30:57 2023] Finished job 144. 647 of 2231 steps (29%) done [Fri Nov 3 10:30:57 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-149.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-149.PRE.gff, analyses/output/Amil-MirMachine/Mir-149.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-149.PRE.unfiltered jobid: 143 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-149.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-149.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-149.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:57 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7383.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7383.PRE.result jobid: 924 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7383.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7383.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:30:58 2023] Finished job 143. 648 of 2231 steps (29%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-149.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:30:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-149.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-149.PRE.filtered.fasta jobid: 1745 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-149.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-149.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-149.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-149.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-149.PRE.filtered.gff jobid: 1186 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-149.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-149.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-149.PRE resources: tmpdir=/tmp [Fri Nov 3 10:30:58 2023] Finished job 1745. 649 of 2231 steps (29%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:30:58 2023] Finished job 1186. 650 of 2231 steps (29%) done [Fri Nov 3 10:31:02 2023] Finished job 204. 651 of 2231 steps (29%) done [Fri Nov 3 10:31:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-188.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-188.PRE.gff, analyses/output/Amil-MirMachine/Mir-188.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-188.PRE.unfiltered jobid: 203 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-188.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-188.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-188.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-346.PRE.CM output: analyses/output/Amil-MirMachine/Mir-346.PRE.result jobid: 548 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-346.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-346.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:03 2023] Finished job 203. 652 of 2231 steps (29%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-188.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-188.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-188.PRE.filtered.gff jobid: 1216 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-188.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-188.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-188.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-188.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-188.PRE.filtered.fasta jobid: 1775 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-188.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-188.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-188.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:03 2023] Finished job 1775. 653 of 2231 steps (29%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:03 2023] Finished job 1216. 654 of 2231 steps (29%) done [Fri Nov 3 10:31:04 2023] Finished job 924. 655 of 2231 steps (29%) done [Fri Nov 3 10:31:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7383.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7383.PRE.gff, analyses/output/Amil-MirMachine/Mir-7383.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7383.PRE.unfiltered jobid: 923 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7383.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7383.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7383.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2705.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2705.PRE.result jobid: 428 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2705.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2705.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:04 2023] Finished job 923. 656 of 2231 steps (29%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7383.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7383.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7383.PRE.filtered.gff jobid: 1576 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7383.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7383.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7383.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7383.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7383.PRE.filtered.fasta jobid: 2135 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7383.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7383.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7383.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:04 2023] Finished job 2135. 657 of 2231 steps (29%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:04 2023] Finished job 1576. 658 of 2231 steps (29%) done [Fri Nov 3 10:31:06 2023] Finished job 548. 659 of 2231 steps (30%) done [Fri Nov 3 10:31:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-346.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-346.PRE.gff, analyses/output/Amil-MirMachine/Mir-346.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-346.PRE.unfiltered jobid: 547 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-346.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-346.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-346.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-540.PRE.CM output: analyses/output/Amil-MirMachine/Mir-540.PRE.result jobid: 744 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-540.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-540.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:06 2023] Finished job 547. 660 of 2231 steps (30%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-346.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-346.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-346.PRE.filtered.gff jobid: 1388 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-346.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-346.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-346.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-346.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-346.PRE.filtered.fasta jobid: 1947 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-346.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-346.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-346.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:07 2023] Finished job 1947. 661 of 2231 steps (30%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:07 2023] Finished job 1388. 662 of 2231 steps (30%) done [Fri Nov 3 10:31:10 2023] Finished job 744. 663 of 2231 steps (30%) done [Fri Nov 3 10:31:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-540.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-540.PRE.gff, analyses/output/Amil-MirMachine/Mir-540.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-540.PRE.unfiltered jobid: 743 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-540.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-540.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-246.PRE.CM output: analyses/output/Amil-MirMachine/Mir-246.PRE.result jobid: 384 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-246.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-246.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:10 2023] Finished job 743. 664 of 2231 steps (30%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-540.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-540.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-540.PRE.filtered.fasta jobid: 2045 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-540.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-540.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-540.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-540.PRE.filtered.gff jobid: 1486 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-540.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-540.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:10 2023] Finished job 2045. 665 of 2231 steps (30%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:10 2023] Finished job 1486. 666 of 2231 steps (30%) done [Fri Nov 3 10:31:15 2023] Finished job 428. 667 of 2231 steps (30%) done [Fri Nov 3 10:31:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2705.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2705.PRE.gff, analyses/output/Amil-MirMachine/Mir-2705.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2705.PRE.unfiltered jobid: 427 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2705.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2705.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2705.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-338.PRE.CM output: analyses/output/Amil-MirMachine/Mir-338.PRE.result jobid: 536 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-338.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-338.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:15 2023] Finished job 427. 668 of 2231 steps (30%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2705.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2705.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2705.PRE.filtered.gff jobid: 1328 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2705.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2705.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2705.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2705.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2705.PRE.filtered.fasta jobid: 1887 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2705.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2705.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2705.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:16 2023] Finished job 1887. 669 of 2231 steps (30%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:16 2023] Finished job 1328. 670 of 2231 steps (30%) done [Fri Nov 3 10:31:23 2023] Finished job 536. 671 of 2231 steps (30%) done [Fri Nov 3 10:31:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-338.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-338.PRE.gff, analyses/output/Amil-MirMachine/Mir-338.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-338.PRE.unfiltered jobid: 535 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-338.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-338.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-338.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1007.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1007.PRE.result jobid: 24 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1007.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1007.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:23 2023] Finished job 535. 672 of 2231 steps (30%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-338.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-338.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-338.PRE.filtered.fasta jobid: 1941 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-338.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-338.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-338.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-338.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-338.PRE.filtered.gff jobid: 1382 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-338.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-338.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-338.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:23 2023] Finished job 1941. 673 of 2231 steps (30%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:24 2023] Finished job 1382. 674 of 2231 steps (30%) done [Fri Nov 3 10:31:25 2023] Finished job 384. 675 of 2231 steps (30%) done [Fri Nov 3 10:31:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-246.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-246.PRE.gff, analyses/output/Amil-MirMachine/Mir-246.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-246.PRE.unfiltered jobid: 383 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-246.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-246.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-246.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2071.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2071.PRE.result jobid: 324 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2071.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2071.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:25 2023] Finished job 383. 676 of 2231 steps (30%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-246.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-246.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-246.PRE.filtered.fasta jobid: 1865 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-246.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-246.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-246.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-246.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-246.PRE.filtered.gff jobid: 1306 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-246.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-246.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-246.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:25 2023] Finished job 1865. 677 of 2231 steps (30%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:25 2023] Finished job 1306. 678 of 2231 steps (30%) done [Fri Nov 3 10:31:28 2023] Finished job 324. 679 of 2231 steps (30%) done [Fri Nov 3 10:31:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2071.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2071.PRE.gff, analyses/output/Amil-MirMachine/Mir-2071.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2071.PRE.unfiltered jobid: 323 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2071.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2071.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2071.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-130.PRE.CM output: analyses/output/Amil-MirMachine/Mir-130.PRE.result jobid: 84 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-130.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-130.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:28 2023] Finished job 323. 680 of 2231 steps (30%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2071.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2071.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2071.PRE.filtered.gff jobid: 1276 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2071.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2071.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2071.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2071.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2071.PRE.filtered.fasta jobid: 1835 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2071.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2071.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2071.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:28 2023] Finished job 1835. 681 of 2231 steps (31%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:29 2023] Finished job 1276. 682 of 2231 steps (31%) done [Fri Nov 3 10:31:30 2023] Finished job 24. 683 of 2231 steps (31%) done [Fri Nov 3 10:31:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1007.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1007.PRE.gff, analyses/output/Amil-MirMachine/Mir-1007.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1007.PRE.unfiltered jobid: 23 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1007.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1007.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1007.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-305.PRE.CM output: analyses/output/Amil-MirMachine/Mir-305.PRE.result jobid: 476 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-305.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-305.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:30 2023] Finished job 23. 684 of 2231 steps (31%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1007.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1007.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1007.PRE.filtered.fasta jobid: 1685 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1007.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1007.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1007.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1007.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1007.PRE.filtered.gff jobid: 1126 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1007.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1007.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1007.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:30 2023] Finished job 1685. 685 of 2231 steps (31%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:31 2023] Finished job 1126. 686 of 2231 steps (31%) done [Fri Nov 3 10:31:35 2023] Finished job 84. 687 of 2231 steps (31%) done [Fri Nov 3 10:31:35 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-130.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-130.PRE.gff, analyses/output/Amil-MirMachine/Mir-130.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-130.PRE.unfiltered jobid: 83 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-130.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-130.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-130.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:35 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-877.PRE.CM output: analyses/output/Amil-MirMachine/Mir-877.PRE.result jobid: 984 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-877.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-877.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:35 2023] Finished job 83. 688 of 2231 steps (31%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-130.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-130.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-130.PRE.filtered.gff jobid: 1156 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-130.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-130.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-130.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-130.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-130.PRE.filtered.fasta jobid: 1715 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-130.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-130.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-130.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:35 2023] Finished job 1715. 689 of 2231 steps (31%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:35 2023] Finished job 1156. 690 of 2231 steps (31%) done [Fri Nov 3 10:31:36 2023] Finished job 476. 691 of 2231 steps (31%) done [Fri Nov 3 10:31:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-305.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-305.PRE.gff, analyses/output/Amil-MirMachine/Mir-305.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-305.PRE.unfiltered jobid: 475 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-305.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-305.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-305.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1301.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1301.PRE.result jobid: 86 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1301.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1301.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:37 2023] Finished job 475. 692 of 2231 steps (31%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-305.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-305.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-305.PRE.filtered.fasta jobid: 1911 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-305.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-305.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-305.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-305.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-305.PRE.filtered.gff jobid: 1352 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-305.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-305.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-305.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:37 2023] Finished job 1911. 693 of 2231 steps (31%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:37 2023] Finished job 1352. 694 of 2231 steps (31%) done [Fri Nov 3 10:31:40 2023] Finished job 984. 695 of 2231 steps (31%) done [Fri Nov 3 10:31:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-877.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-877.PRE.gff, analyses/output/Amil-MirMachine/Mir-877.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-877.PRE.unfiltered jobid: 983 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-877.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-877.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-877.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-456.PRE.CM output: analyses/output/Amil-MirMachine/Mir-456.PRE.result jobid: 626 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-456.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-456.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:40 2023] Finished job 983. 696 of 2231 steps (31%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-877.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-877.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-877.PRE.filtered.fasta jobid: 2165 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-877.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-877.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-877.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-877.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-877.PRE.filtered.gff jobid: 1606 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-877.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-877.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-877.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:40 2023] Finished job 2165. 697 of 2231 steps (31%) done Select jobs to execute... [Fri Nov 3 10:31:40 2023] Finished job 86. 698 of 2231 steps (31%) done [Fri Nov 3 10:31:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-490.PRE.CM output: analyses/output/Amil-MirMachine/Mir-490.PRE.result jobid: 716 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-490.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-490.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1301.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1301.PRE.gff, analyses/output/Amil-MirMachine/Mir-1301.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1301.PRE.unfiltered jobid: 85 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1301.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1301.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1301.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:31:40 2023] Finished job 85. ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] 699 of 2231 steps (31%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1301.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1301.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1301.PRE.filtered.fasta jobid: 1716 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1301.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1301.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1301.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1301.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1301.PRE.filtered.gff jobid: 1157 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1301.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1301.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1301.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:40 2023] Finished job 1606. 700 of 2231 steps (31%) done Select jobs to execute... [Fri Nov 3 10:31:40 2023] Finished job 1716. 701 of 2231 steps (31%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:41 2023] Finished job 1157. 702 of 2231 steps (31%) done [Fri Nov 3 10:31:44 2023] Finished job 626. 703 of 2231 steps (32%) done [Fri Nov 3 10:31:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-456.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-456.PRE.gff, analyses/output/Amil-MirMachine/Mir-456.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-456.PRE.unfiltered jobid: 625 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-456.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-456.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-456.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-728.PRE.CM output: analyses/output/Amil-MirMachine/Mir-728.PRE.result jobid: 866 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-728.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-728.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:44 2023] Finished job 625. 704 of 2231 steps (32%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-456.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-456.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-456.PRE.filtered.fasta jobid: 1986 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-456.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-456.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-456.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-456.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-456.PRE.filtered.gff jobid: 1427 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-456.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-456.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-456.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:44 2023] Finished job 1986. 705 of 2231 steps (32%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:45 2023] Finished job 1427. 706 of 2231 steps (32%) done [Fri Nov 3 10:31:45 2023] Finished job 716. 707 of 2231 steps (32%) done [Fri Nov 3 10:31:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-490.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-490.PRE.gff, analyses/output/Amil-MirMachine/Mir-490.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-490.PRE.unfiltered jobid: 715 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-490.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-490.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-490.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-15.PRE.CM output: analyses/output/Amil-MirMachine/Mir-15.PRE.result jobid: 146 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-15.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-15.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:45 2023] Finished job 715. 708 of 2231 steps (32%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-490.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-490.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-490.PRE.filtered.fasta jobid: 2031 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-490.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-490.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-490.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-490.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-490.PRE.filtered.gff jobid: 1472 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-490.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-490.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-490.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:45 2023] Finished job 2031. 709 of 2231 steps (32%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:46 2023] Finished job 1472. 710 of 2231 steps (32%) done [Fri Nov 3 10:31:54 2023] Finished job 146. 711 of 2231 steps (32%) done [Fri Nov 3 10:31:54 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-15.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-15.PRE.gff, analyses/output/Amil-MirMachine/Mir-15.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-15.PRE.unfiltered jobid: 145 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-15.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-15.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-15.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:54 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-19.PRE.CM output: analyses/output/Amil-MirMachine/Mir-19.PRE.result jobid: 206 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-19.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-19.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:54 2023] Finished job 145. 712 of 2231 steps (32%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-15.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:54 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-15.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-15.PRE.filtered.fasta jobid: 1746 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-15.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-15.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-15.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:54 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-15.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-15.PRE.filtered.gff jobid: 1187 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-15.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-15.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-15.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:54 2023] Finished job 1746. 713 of 2231 steps (32%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:54 2023] Finished job 1187. 714 of 2231 steps (32%) done [Fri Nov 3 10:31:55 2023] Finished job 866. 715 of 2231 steps (32%) done [Fri Nov 3 10:31:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-579.PRE.CM output: analyses/output/Amil-MirMachine/Mir-579.PRE.result jobid: 764 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-579.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-579.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:31:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-728.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-728.PRE.gff, analyses/output/Amil-MirMachine/Mir-728.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-728.PRE.unfiltered jobid: 865 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-728.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-728.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-728.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:55 2023] Finished job 865. 716 of 2231 steps (32%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-728.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:31:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-728.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-728.PRE.filtered.fasta jobid: 2106 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-728.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-728.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-728.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-728.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-728.PRE.filtered.gff jobid: 1547 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-728.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-728.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-728.PRE resources: tmpdir=/tmp [Fri Nov 3 10:31:55 2023] Finished job 2106. 717 of 2231 steps (32%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:31:55 2023] Finished job 1547. 718 of 2231 steps (32%) done [Fri Nov 3 10:32:00 2023] Finished job 764. 719 of 2231 steps (32%) done [Fri Nov 3 10:32:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7385.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7385.PRE.result jobid: 926 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7385.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7385.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-579.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-579.PRE.gff, analyses/output/Amil-MirMachine/Mir-579.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-579.PRE.unfiltered jobid: 763 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-579.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-579.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-579.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:01 2023] Finished job 763. 720 of 2231 steps (32%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-579.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-579.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-579.PRE.filtered.gff jobid: 1496 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-579.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-579.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-579.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-579.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-579.PRE.filtered.fasta jobid: 2055 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-579.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-579.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-579.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:01 2023] Finished job 2055. 721 of 2231 steps (32%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:01 2023] Finished job 1496. 722 of 2231 steps (32%) done [Fri Nov 3 10:32:04 2023] Finished job 206. 723 of 2231 steps (32%) done [Fri Nov 3 10:32:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7147.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7147.PRE.result jobid: 836 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7147.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7147.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-19.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-19.PRE.gff, analyses/output/Amil-MirMachine/Mir-19.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-19.PRE.unfiltered jobid: 205 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-19.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-19.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-19.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:04 2023] Finished job 205. 724 of 2231 steps (32%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-19.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-19.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-19.PRE.filtered.fasta jobid: 1776 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-19.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-19.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-19.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-19.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-19.PRE.filtered.gff jobid: 1217 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-19.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-19.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-19.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:04 2023] Finished job 1776. 725 of 2231 steps (32%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:04 2023] Finished job 1217. 726 of 2231 steps (33%) done [Fri Nov 3 10:32:08 2023] Finished job 926. 727 of 2231 steps (33%) done [Fri Nov 3 10:32:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7392.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7392.PRE.result jobid: 928 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7392.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7392.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7385.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7385.PRE.gff, analyses/output/Amil-MirMachine/Mir-7385.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7385.PRE.unfiltered jobid: 925 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7385.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7385.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7385.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:08 2023] Finished job 925. 728 of 2231 steps (33%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7385.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7385.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7385.PRE.filtered.fasta jobid: 2136 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7385.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7385.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7385.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7385.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7385.PRE.filtered.gff jobid: 1577 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7385.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7385.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7385.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:08 2023] Finished job 2136. 729 of 2231 steps (33%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:09 2023] Finished job 1577. 730 of 2231 steps (33%) done [Fri Nov 3 10:32:10 2023] Finished job 836. 731 of 2231 steps (33%) done [Fri Nov 3 10:32:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7147.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7147.PRE.gff, analyses/output/Amil-MirMachine/Mir-7147.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7147.PRE.unfiltered jobid: 835 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7147.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7147.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7147.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-430.PRE.CM output: analyses/output/Amil-MirMachine/Mir-430.PRE.result jobid: 596 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-430.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-430.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:10 2023] Finished job 835. 732 of 2231 steps (33%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7147.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7147.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7147.PRE.filtered.fasta jobid: 2091 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7147.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7147.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7147.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7147.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7147.PRE.filtered.gff jobid: 1532 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7147.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7147.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7147.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:10 2023] Finished job 2091. 733 of 2231 steps (33%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:10 2023] Finished job 1532. 734 of 2231 steps (33%) done [Fri Nov 3 10:32:13 2023] Finished job 928. 735 of 2231 steps (33%) done [Fri Nov 3 10:32:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-248.PRE.CM output: analyses/output/Amil-MirMachine/Mir-248.PRE.result jobid: 386 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-248.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-248.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7392.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7392.PRE.gff, analyses/output/Amil-MirMachine/Mir-7392.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7392.PRE.unfiltered jobid: 927 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7392.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7392.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7392.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:13 2023] Finished job 927. 736 of 2231 steps (33%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7392.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7392.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7392.PRE.filtered.gff jobid: 1578 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7392.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7392.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7392.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7392.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7392.PRE.filtered.fasta jobid: 2137 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7392.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7392.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7392.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:14 2023] Finished job 2137. 737 of 2231 steps (33%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:14 2023] Finished job 1578. 738 of 2231 steps (33%) done [Fri Nov 3 10:32:20 2023] Finished job 386. 739 of 2231 steps (33%) done [Fri Nov 3 10:32:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-248.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-248.PRE.gff, analyses/output/Amil-MirMachine/Mir-248.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-248.PRE.unfiltered jobid: 385 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-248.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-248.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-248.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2072.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2072.PRE.result jobid: 326 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2072.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2072.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] Finished job 596. 740 of 2231 steps (33%) done Select jobs to execute... [Fri Nov 3 10:32:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-430.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-430.PRE.gff, analyses/output/Amil-MirMachine/Mir-430.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-430.PRE.unfiltered jobid: 595 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-430.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-430.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-430.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-541.PRE.CM output: analyses/output/Amil-MirMachine/Mir-541.PRE.result jobid: 746 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-541.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-541.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] Finished job 385. 741 of 2231 steps (33%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-248.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-248.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-248.PRE.filtered.fasta jobid: 1866 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-248.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-248.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-248.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-248.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-248.PRE.filtered.gff jobid: 1307 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-248.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-248.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-248.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] Finished job 595. 742 of 2231 steps (33%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-430.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-430.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-430.PRE.filtered.fasta jobid: 1971 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-430.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-430.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-430.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-430.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-430.PRE.filtered.gff jobid: 1412 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-430.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-430.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-430.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:20 2023] Finished job 1866. 743 of 2231 steps (33%) done Select jobs to execute... [Fri Nov 3 10:32:20 2023] Finished job 1971. 744 of 2231 steps (33%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:32:20 2023] Finished job 1307. 745 of 2231 steps (33%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:20 2023] Finished job 1412. 746 of 2231 steps (33%) done [Fri Nov 3 10:32:23 2023] Finished job 326. 747 of 2231 steps (33%) done [Fri Nov 3 10:32:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9717.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9717.PRE.result jobid: 1074 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9717.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9717.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2072.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2072.PRE.gff, analyses/output/Amil-MirMachine/Mir-2072.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2072.PRE.unfiltered jobid: 325 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2072.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2072.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2072.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:24 2023] Finished job 325. 748 of 2231 steps (34%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2072.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2072.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2072.PRE.filtered.fasta jobid: 1836 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2072.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2072.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2072.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2072.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2072.PRE.filtered.gff jobid: 1277 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2072.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2072.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2072.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:24 2023] Finished job 1836. 749 of 2231 steps (34%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:24 2023] Finished job 1277. 750 of 2231 steps (34%) done [Fri Nov 3 10:32:27 2023] Finished job 1074. 751 of 2231 steps (34%) done [Fri Nov 3 10:32:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9717.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9717.PRE.gff, analyses/output/Amil-MirMachine/Mir-9717.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9717.PRE.unfiltered jobid: 1073 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9717.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9717.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9717.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-101.PRE.CM output: analyses/output/Amil-MirMachine/Mir-101.PRE.result jobid: 26 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-101.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-101.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:27 2023] Finished job 1073. 752 of 2231 steps (34%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9717.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9717.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9717.PRE.filtered.fasta jobid: 2210 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9717.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9717.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9717.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9717.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9717.PRE.filtered.gff jobid: 1651 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9717.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9717.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9717.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:28 2023] Finished job 2210. 753 of 2231 steps (34%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:28 2023] Finished job 746. 754 of 2231 steps (34%) done [Fri Nov 3 10:32:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-541.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-541.PRE.gff, analyses/output/Amil-MirMachine/Mir-541.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-541.PRE.unfiltered jobid: 745 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-541.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-541.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-879.PRE.CM output: analyses/output/Amil-MirMachine/Mir-879.PRE.result jobid: 986 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-879.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-879.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:28 2023] Finished job 1651. 755 of 2231 steps (34%) done Select jobs to execute... [Fri Nov 3 10:32:28 2023] Finished job 745. 756 of 2231 steps (34%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-541.PRE.ext.gff. [Fri Nov 3 10:32:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-541.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-541.PRE.filtered.fasta jobid: 2046 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-541.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-541.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-541.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-541.PRE.filtered.gff jobid: 1487 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-541.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-541.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:28 2023] Finished job 2046. 757 of 2231 steps (34%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:28 2023] Finished job 1487. 758 of 2231 steps (34%) done [Fri Nov 3 10:32:32 2023] Finished job 986. 759 of 2231 steps (34%) done [Fri Nov 3 10:32:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-879.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-879.PRE.gff, analyses/output/Amil-MirMachine/Mir-879.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-879.PRE.unfiltered jobid: 985 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-879.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-879.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-879.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7398.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7398.PRE.result jobid: 934 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7398.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7398.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:32 2023] Finished job 985. 760 of 2231 steps (34%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-879.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-879.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-879.PRE.filtered.fasta jobid: 2166 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-879.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-879.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-879.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-879.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-879.PRE.filtered.gff jobid: 1607 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-879.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-879.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-879.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:33 2023] Finished job 2166. 761 of 2231 steps (34%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:33 2023] Finished job 1607. 762 of 2231 steps (34%) done [Fri Nov 3 10:32:33 2023] Finished job 26. 763 of 2231 steps (34%) done [Fri Nov 3 10:32:33 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7133.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7133.PRE.result jobid: 834 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7133.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7133.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:33 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-101.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-101.PRE.gff, analyses/output/Amil-MirMachine/Mir-101.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-101.PRE.unfiltered jobid: 25 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-101.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-101.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-101.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:33 2023] Finished job 25. 764 of 2231 steps (34%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-101.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-101.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-101.PRE.filtered.fasta jobid: 1686 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-101.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-101.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-101.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-101.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-101.PRE.filtered.gff jobid: 1127 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-101.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-101.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-101.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:34 2023] Finished job 1686. 765 of 2231 steps (34%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:34 2023] Finished job 1127. 766 of 2231 steps (34%) done [Fri Nov 3 10:32:39 2023] Finished job 934. 767 of 2231 steps (34%) done [Fri Nov 3 10:32:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1546.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1546.PRE.result jobid: 160 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1546.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1546.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7398.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7398.PRE.gff, analyses/output/Amil-MirMachine/Mir-7398.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7398.PRE.unfiltered jobid: 933 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7398.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7398.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7398.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:39 2023] Finished job 933. 768 of 2231 steps (34%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7398.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7398.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7398.PRE.filtered.fasta jobid: 2140 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7398.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7398.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7398.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7398.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7398.PRE.filtered.gff jobid: 1581 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7398.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7398.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7398.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:39 2023] Finished job 2140. 769 of 2231 steps (34%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:39 2023] Finished job 1581. 770 of 2231 steps (35%) done [Fri Nov 3 10:32:44 2023] Finished job 834. 771 of 2231 steps (35%) done [Fri Nov 3 10:32:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-542.PRE.CM output: analyses/output/Amil-MirMachine/Mir-542.PRE.result jobid: 748 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-542.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-542.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7133.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7133.PRE.gff, analyses/output/Amil-MirMachine/Mir-7133.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7133.PRE.unfiltered jobid: 833 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7133.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7133.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7133.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:44 2023] Finished job 833. 772 of 2231 steps (35%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7133.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7133.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7133.PRE.filtered.gff jobid: 1531 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7133.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7133.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7133.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7133.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7133.PRE.filtered.fasta jobid: 2090 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7133.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7133.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7133.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:44 2023] Finished job 2090. 773 of 2231 steps (35%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:44 2023] Finished job 1531. 774 of 2231 steps (35%) done [Fri Nov 3 10:32:45 2023] Finished job 160. 775 of 2231 steps (35%) done [Fri Nov 3 10:32:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1010.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1010.PRE.result jobid: 28 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1010.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1010.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1546.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1546.PRE.gff, analyses/output/Amil-MirMachine/Mir-1546.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1546.PRE.unfiltered jobid: 159 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1546.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1546.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1546.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:45 2023] Finished job 159. 776 of 2231 steps (35%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1546.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1546.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1546.PRE.filtered.fasta jobid: 1753 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1546.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1546.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1546.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1546.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1546.PRE.filtered.gff jobid: 1194 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1546.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1546.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1546.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:45 2023] Finished job 1753. 777 of 2231 steps (35%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:45 2023] Finished job 1194. 778 of 2231 steps (35%) done [Fri Nov 3 10:32:49 2023] Finished job 748. 779 of 2231 steps (35%) done [Fri Nov 3 10:32:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4838.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4838.PRE.result jobid: 664 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4838.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4838.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-542.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-542.PRE.gff, analyses/output/Amil-MirMachine/Mir-542.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-542.PRE.unfiltered jobid: 747 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-542.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-542.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:49 2023] Finished job 747. 780 of 2231 steps (35%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-542.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-542.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-542.PRE.filtered.gff jobid: 1488 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-542.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-542.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-542.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-542.PRE.filtered.fasta jobid: 2047 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-542.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-542.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:49 2023] Finished job 2047. 781 of 2231 steps (35%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:50 2023] Finished job 1488. 782 of 2231 steps (35%) done [Fri Nov 3 10:32:53 2023] Finished job 28. 783 of 2231 steps (35%) done [Fri Nov 3 10:32:54 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1306.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1306.PRE.result jobid: 88 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1306.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1306.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:54 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1010.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1010.PRE.gff, analyses/output/Amil-MirMachine/Mir-1010.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1010.PRE.unfiltered jobid: 27 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1010.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1010.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1010.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:54 2023] Finished job 27. 784 of 2231 steps (35%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1010.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:54 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1010.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1010.PRE.filtered.gff jobid: 1128 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1010.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1010.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1010.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:54 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1010.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1010.PRE.filtered.fasta jobid: 1687 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1010.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1010.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1010.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:54 2023] Finished job 1687. 785 of 2231 steps (35%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:54 2023] Finished job 1128. 786 of 2231 steps (35%) done [Fri Nov 3 10:32:55 2023] Finished job 664. 787 of 2231 steps (35%) done [Fri Nov 3 10:32:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2693.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2693.PRE.result jobid: 424 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2693.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2693.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4838.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4838.PRE.gff, analyses/output/Amil-MirMachine/Mir-4838.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4838.PRE.unfiltered jobid: 663 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4838.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4838.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4838.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:56 2023] Finished job 663. 788 of 2231 steps (35%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4838.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4838.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4838.PRE.filtered.gff jobid: 1446 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4838.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4838.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4838.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4838.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4838.PRE.filtered.fasta jobid: 2005 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4838.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4838.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4838.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:56 2023] Finished job 2005. 789 of 2231 steps (35%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:56 2023] Finished job 1446. 790 of 2231 steps (35%) done [Fri Nov 3 10:32:57 2023] Finished job 88. 791 of 2231 steps (35%) done [Fri Nov 3 10:32:57 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-628.PRE.CM output: analyses/output/Amil-MirMachine/Mir-628.PRE.result jobid: 788 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-628.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-628.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:32:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1306.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1306.PRE.gff, analyses/output/Amil-MirMachine/Mir-1306.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1306.PRE.unfiltered jobid: 87 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1306.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1306.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1306.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:58 2023] Finished job 87. 792 of 2231 steps (35%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1306.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:32:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1306.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1306.PRE.filtered.gff jobid: 1158 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1306.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1306.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1306.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1306.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1306.PRE.filtered.fasta jobid: 1717 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1306.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1306.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1306.PRE resources: tmpdir=/tmp [Fri Nov 3 10:32:58 2023] Finished job 1717. 793 of 2231 steps (36%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:32:58 2023] Finished job 1158. 794 of 2231 steps (36%) done [Fri Nov 3 10:33:01 2023] Finished job 424. 795 of 2231 steps (36%) done [Fri Nov 3 10:33:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-199.PRE.CM output: analyses/output/Amil-MirMachine/Mir-199.PRE.result jobid: 240 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-199.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-199.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2693.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2693.PRE.gff, analyses/output/Amil-MirMachine/Mir-2693.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2693.PRE.unfiltered jobid: 423 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2693.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2693.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2693.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:01 2023] Finished job 423. 796 of 2231 steps (36%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2693.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2693.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2693.PRE.filtered.gff jobid: 1326 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2693.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2693.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2693.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2693.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2693.PRE.filtered.fasta jobid: 1885 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2693.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2693.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2693.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:01 2023] Finished job 1885. 797 of 2231 steps (36%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:02 2023] Finished job 1326. 798 of 2231 steps (36%) done [Fri Nov 3 10:33:03 2023] Finished job 788. 799 of 2231 steps (36%) done [Fri Nov 3 10:33:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-628.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-628.PRE.gff, analyses/output/Amil-MirMachine/Mir-628.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-628.PRE.unfiltered jobid: 787 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-628.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-628.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-628.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-306.PRE.CM output: analyses/output/Amil-MirMachine/Mir-306.PRE.result jobid: 480 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-306.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-306.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:03 2023] Finished job 787. 800 of 2231 steps (36%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-628.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-628.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-628.PRE.filtered.gff jobid: 1508 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-628.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-628.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-628.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-628.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-628.PRE.filtered.fasta jobid: 2067 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-628.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-628.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-628.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:03 2023] Finished job 2067. 801 of 2231 steps (36%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:04 2023] Finished job 1508. 802 of 2231 steps (36%) done [Fri Nov 3 10:33:07 2023] Finished job 240. 803 of 2231 steps (36%) done [Fri Nov 3 10:33:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2076.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2076.PRE.result jobid: 328 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2076.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2076.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-199.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-199.PRE.gff, analyses/output/Amil-MirMachine/Mir-199.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-199.PRE.unfiltered jobid: 239 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-199.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-199.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-199.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:07 2023] Finished job 239. 804 of 2231 steps (36%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-199.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-199.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-199.PRE.filtered.gff jobid: 1234 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-199.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-199.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-199.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-199.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-199.PRE.filtered.fasta jobid: 1793 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-199.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-199.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-199.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:07 2023] Finished job 1793. 805 of 2231 steps (36%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:08 2023] Finished job 1234. 806 of 2231 steps (36%) done [Fri Nov 3 10:33:12 2023] Finished job 480. 807 of 2231 steps (36%) done [Fri Nov 3 10:33:12 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-34.PRE.CM output: analyses/output/Amil-MirMachine/Mir-34.PRE.result jobid: 540 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-34.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-34.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:12 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-306.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-306.PRE.gff, analyses/output/Amil-MirMachine/Mir-306.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-306.PRE.unfiltered jobid: 479 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-306.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-306.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-306.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:12 2023] Finished job 479. 808 of 2231 steps (36%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-306.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:12 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-306.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-306.PRE.filtered.gff jobid: 1354 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-306.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-306.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-306.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:12 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-306.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-306.PRE.filtered.fasta jobid: 1913 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-306.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-306.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-306.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:12 2023] Finished job 1913. 809 of 2231 steps (36%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:12 2023] Finished job 1354. 810 of 2231 steps (36%) done [Fri Nov 3 10:33:13 2023] Finished job 328. 811 of 2231 steps (36%) done [Fri Nov 3 10:33:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-458.PRE.CM output: analyses/output/Amil-MirMachine/Mir-458.PRE.result jobid: 628 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-458.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-458.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2076.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2076.PRE.gff, analyses/output/Amil-MirMachine/Mir-2076.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2076.PRE.unfiltered jobid: 327 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2076.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2076.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2076.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:13 2023] Finished job 327. 812 of 2231 steps (36%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2076.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2076.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2076.PRE.filtered.gff jobid: 1278 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2076.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2076.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2076.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2076.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2076.PRE.filtered.fasta jobid: 1837 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2076.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2076.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2076.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:13 2023] Finished job 1837. 813 of 2231 steps (36%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:13 2023] Finished job 1278. 814 of 2231 steps (36%) done [Fri Nov 3 10:33:17 2023] Finished job 540. 815 of 2231 steps (37%) done [Fri Nov 3 10:33:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-150.PRE.CM output: analyses/output/Amil-MirMachine/Mir-150.PRE.result jobid: 148 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-150.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-150.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-34.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-34.PRE.gff, analyses/output/Amil-MirMachine/Mir-34.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-34.PRE.unfiltered jobid: 539 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-34.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-34.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-34.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:17 2023] Finished job 539. 816 of 2231 steps (37%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-34.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-34.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-34.PRE.filtered.fasta jobid: 1943 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-34.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-34.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-34.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-34.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-34.PRE.filtered.gff jobid: 1384 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-34.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-34.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-34.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:17 2023] Finished job 1943. 817 of 2231 steps (37%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:18 2023] Finished job 1384. 818 of 2231 steps (37%) done [Fri Nov 3 10:33:22 2023] Finished job 148. 819 of 2231 steps (37%) done [Fri Nov 3 10:33:22 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-887.PRE.CM output: analyses/output/Amil-MirMachine/Mir-887.PRE.result jobid: 990 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-887.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-887.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:22 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-150.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-150.PRE.gff, analyses/output/Amil-MirMachine/Mir-150.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-150.PRE.unfiltered jobid: 147 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-150.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-150.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-150.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:22 2023] Finished job 147. 820 of 2231 steps (37%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-150.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:22 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-150.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-150.PRE.filtered.gff jobid: 1188 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-150.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-150.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-150.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:22 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-150.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-150.PRE.filtered.fasta jobid: 1747 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-150.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-150.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-150.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:22 2023] Finished job 1747. 821 of 2231 steps (37%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:23 2023] Finished job 1188. 822 of 2231 steps (37%) done [Fri Nov 3 10:33:23 2023] Finished job 628. 823 of 2231 steps (37%) done [Fri Nov 3 10:33:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-459.PRE.CM output: analyses/output/Amil-MirMachine/Mir-459.PRE.result jobid: 630 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-459.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-459.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-458.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-458.PRE.gff, analyses/output/Amil-MirMachine/Mir-458.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-458.PRE.unfiltered jobid: 627 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-458.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-458.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-458.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:23 2023] Finished job 627. 824 of 2231 steps (37%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-458.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-458.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-458.PRE.filtered.gff jobid: 1428 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-458.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-458.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-458.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-458.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-458.PRE.filtered.fasta jobid: 1987 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-458.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-458.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-458.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:23 2023] Finished job 1987. 825 of 2231 steps (37%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:23 2023] Finished job 1428. 826 of 2231 steps (37%) done [Fri Nov 3 10:33:26 2023] Finished job 990. 827 of 2231 steps (37%) done [Fri Nov 3 10:33:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2483.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2483.PRE.result jobid: 388 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2483.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2483.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-887.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-887.PRE.gff, analyses/output/Amil-MirMachine/Mir-887.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-887.PRE.unfiltered jobid: 989 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-887.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-887.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-887.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:26 2023] Finished job 989. 828 of 2231 steps (37%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-887.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-887.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-887.PRE.filtered.gff jobid: 1609 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-887.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-887.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-887.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-887.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-887.PRE.filtered.fasta jobid: 2168 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-887.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-887.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-887.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:26 2023] Finished job 2168. 829 of 2231 steps (37%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:26 2023] Finished job 1609. 830 of 2231 steps (37%) done [Fri Nov 3 10:33:30 2023] Finished job 388. 831 of 2231 steps (37%) done [Fri Nov 3 10:33:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7284.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7284.PRE.result jobid: 870 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7284.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7284.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2483.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2483.PRE.gff, analyses/output/Amil-MirMachine/Mir-2483.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2483.PRE.unfiltered jobid: 387 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2483.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2483.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2483.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:31 2023] Finished job 387. 832 of 2231 steps (37%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2483.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2483.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2483.PRE.filtered.gff jobid: 1308 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2483.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2483.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2483.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2483.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2483.PRE.filtered.fasta jobid: 1867 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2483.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2483.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2483.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:31 2023] Finished job 1867. 833 of 2231 steps (37%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:31 2023] Finished job 630. 834 of 2231 steps (37%) done [Fri Nov 3 10:33:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-459.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-459.PRE.gff, analyses/output/Amil-MirMachine/Mir-459.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-459.PRE.unfiltered jobid: 629 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-459.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-459.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-459.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-153.PRE.CM output: analyses/output/Amil-MirMachine/Mir-153.PRE.result jobid: 150 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-153.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-153.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:31 2023] Finished job 1308. 835 of 2231 steps (37%) done Select jobs to execute... [Fri Nov 3 10:33:31 2023] Finished job 629. 836 of 2231 steps (37%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-459.PRE.ext.gff. [Fri Nov 3 10:33:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-459.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-459.PRE.filtered.gff jobid: 1429 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-459.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-459.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-459.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-459.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-459.PRE.filtered.fasta jobid: 1988 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-459.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-459.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-459.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:31 2023] Finished job 1988. 837 of 2231 steps (38%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:31 2023] Finished job 1429. 838 of 2231 steps (38%) done [Fri Nov 3 10:33:38 2023] Finished job 870. 839 of 2231 steps (38%) done [Fri Nov 3 10:33:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7284.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7284.PRE.gff, analyses/output/Amil-MirMachine/Mir-7284.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7284.PRE.unfiltered jobid: 869 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7284.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7284.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7284.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-191.PRE.CM output: analyses/output/Amil-MirMachine/Mir-191.PRE.result jobid: 210 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-191.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-191.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:38 2023] Finished job 869. 840 of 2231 steps (38%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7284.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7284.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7284.PRE.filtered.gff jobid: 1549 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7284.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7284.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7284.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7284.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7284.PRE.filtered.fasta jobid: 2108 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7284.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7284.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7284.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:39 2023] Finished job 2108. 841 of 2231 steps (38%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:39 2023] Finished job 1549. 842 of 2231 steps (38%) done [Fri Nov 3 10:33:46 2023] Finished job 150. 843 of 2231 steps (38%) done [Fri Nov 3 10:33:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7281.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7281.PRE.result jobid: 868 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7281.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7281.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-153.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-153.PRE.gff, analyses/output/Amil-MirMachine/Mir-153.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-153.PRE.unfiltered jobid: 149 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-153.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-153.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-153.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:46 2023] Finished job 149. 844 of 2231 steps (38%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-153.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-153.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-153.PRE.filtered.gff jobid: 1189 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-153.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-153.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-153.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-153.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-153.PRE.filtered.fasta jobid: 1748 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-153.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-153.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-153.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:46 2023] Finished job 1748. 845 of 2231 steps (38%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:47 2023] Finished job 1189. 846 of 2231 steps (38%) done [Fri Nov 3 10:33:48 2023] Finished job 210. 847 of 2231 steps (38%) done [Fri Nov 3 10:33:48 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-191.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-191.PRE.gff, analyses/output/Amil-MirMachine/Mir-191.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-191.PRE.unfiltered jobid: 209 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-191.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-191.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-191.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:48 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7394.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7394.PRE.result jobid: 930 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7394.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7394.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:48 2023] Finished job 209. 848 of 2231 steps (38%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-191.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:48 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-191.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-191.PRE.filtered.gff jobid: 1219 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-191.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-191.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-191.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:48 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-191.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-191.PRE.filtered.fasta jobid: 1778 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-191.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-191.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-191.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:48 2023] Finished job 1778. 849 of 2231 steps (38%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:48 2023] Finished job 1219. 850 of 2231 steps (38%) done [Fri Nov 3 10:33:51 2023] Finished job 868. 851 of 2231 steps (38%) done [Fri Nov 3 10:33:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-190.PRE.CM output: analyses/output/Amil-MirMachine/Mir-190.PRE.result jobid: 208 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-190.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-190.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7281.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7281.PRE.gff, analyses/output/Amil-MirMachine/Mir-7281.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7281.PRE.unfiltered jobid: 867 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7281.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7281.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7281.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:51 2023] Finished job 867. 852 of 2231 steps (38%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7281.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7281.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7281.PRE.filtered.gff jobid: 1548 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7281.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7281.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7281.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7281.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7281.PRE.filtered.fasta jobid: 2107 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7281.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7281.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7281.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:51 2023] Finished job 2107. 853 of 2231 steps (38%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:52 2023] Finished job 1548. 854 of 2231 steps (38%) done [Fri Nov 3 10:33:55 2023] Finished job 930. 855 of 2231 steps (38%) done [Fri Nov 3 10:33:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7394.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7394.PRE.gff, analyses/output/Amil-MirMachine/Mir-7394.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7394.PRE.unfiltered jobid: 929 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7394.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7394.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7394.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-544.PRE.CM output: analyses/output/Amil-MirMachine/Mir-544.PRE.result jobid: 750 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-544.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-544.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:33:55 2023] Finished job 929. 856 of 2231 steps (38%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7394.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:33:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7394.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7394.PRE.filtered.gff jobid: 1579 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7394.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7394.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7394.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7394.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7394.PRE.filtered.fasta jobid: 2138 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7394.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7394.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7394.PRE resources: tmpdir=/tmp [Fri Nov 3 10:33:55 2023] Finished job 2138. 857 of 2231 steps (38%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:33:56 2023] Finished job 1579. 858 of 2231 steps (38%) done [Fri Nov 3 10:34:00 2023] Finished job 208. 859 of 2231 steps (39%) done [Fri Nov 3 10:34:00 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-885.PRE.CM output: analyses/output/Amil-MirMachine/Mir-885.PRE.result jobid: 988 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-885.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-885.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:00 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-190.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-190.PRE.gff, analyses/output/Amil-MirMachine/Mir-190.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-190.PRE.unfiltered jobid: 207 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-190.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-190.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-190.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:00 2023] Finished job 207. 860 of 2231 steps (39%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-190.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:00 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-190.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-190.PRE.filtered.gff jobid: 1218 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-190.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-190.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-190.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:00 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-190.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-190.PRE.filtered.fasta jobid: 1777 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-190.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-190.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-190.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:00 2023] Finished job 1777. 861 of 2231 steps (39%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:00 2023] Finished job 1218. 862 of 2231 steps (39%) done [Fri Nov 3 10:34:04 2023] Finished job 750. 863 of 2231 steps (39%) done [Fri Nov 3 10:34:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-544.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-544.PRE.gff, analyses/output/Amil-MirMachine/Mir-544.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-544.PRE.unfiltered jobid: 749 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-544.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-544.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-544.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-103.PRE.CM output: analyses/output/Amil-MirMachine/Mir-103.PRE.result jobid: 30 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-103.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-103.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] Finished job 749. 864 of 2231 steps (39%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-544.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-544.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-544.PRE.filtered.gff jobid: 1489 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-544.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-544.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-544.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-544.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-544.PRE.filtered.fasta jobid: 2048 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-544.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-544.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-544.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] Finished job 2048. 865 of 2231 steps (39%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:34:04 2023] Finished job 988. 866 of 2231 steps (39%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-208.PRE.CM output: analyses/output/Amil-MirMachine/Mir-208.PRE.result jobid: 330 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-208.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-208.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-885.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-885.PRE.gff, analyses/output/Amil-MirMachine/Mir-885.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-885.PRE.unfiltered jobid: 987 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-885.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-885.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-885.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] Finished job 1489. 867 of 2231 steps (39%) done Select jobs to execute... [Fri Nov 3 10:34:04 2023] Finished job 987. 868 of 2231 steps (39%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-885.PRE.ext.gff. [Fri Nov 3 10:34:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-885.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-885.PRE.filtered.gff jobid: 1608 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-885.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-885.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-885.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-885.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-885.PRE.filtered.fasta jobid: 2167 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-885.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-885.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-885.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:04 2023] Finished job 2167. 869 of 2231 steps (39%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:05 2023] Finished job 1608. 870 of 2231 steps (39%) done [Fri Nov 3 10:34:10 2023] Finished job 30. 871 of 2231 steps (39%) done [Fri Nov 3 10:34:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-103.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-103.PRE.gff, analyses/output/Amil-MirMachine/Mir-103.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-103.PRE.unfiltered jobid: 29 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-103.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-103.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-103.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1307.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1307.PRE.result jobid: 90 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1307.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1307.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:10 2023] Finished job 29. 872 of 2231 steps (39%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-103.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-103.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-103.PRE.filtered.gff jobid: 1129 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-103.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-103.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-103.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-103.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-103.PRE.filtered.fasta jobid: 1688 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-103.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-103.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-103.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:10 2023] Finished job 1688. 873 of 2231 steps (39%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:11 2023] Finished job 1129. 874 of 2231 steps (39%) done [Fri Nov 3 10:34:14 2023] Finished job 90. 875 of 2231 steps (39%) done [Fri Nov 3 10:34:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1307.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1307.PRE.gff, analyses/output/Amil-MirMachine/Mir-1307.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1307.PRE.unfiltered jobid: 89 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1307.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1307.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1307.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-137.PRE.CM output: analyses/output/Amil-MirMachine/Mir-137.PRE.result jobid: 108 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-137.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-137.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] Finished job 89. 876 of 2231 steps (39%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1307.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1307.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1307.PRE.filtered.gff jobid: 1159 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1307.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1307.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1307.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1307.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1307.PRE.filtered.fasta jobid: 1718 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1307.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1307.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1307.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] Finished job 1718. 877 of 2231 steps (39%) done Select jobs to execute... [Fri Nov 3 10:34:15 2023] Finished job 330. 878 of 2231 steps (39%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-208.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-208.PRE.gff, analyses/output/Amil-MirMachine/Mir-208.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-208.PRE.unfiltered jobid: 329 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-208.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-208.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-208.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9.PRE.result jobid: 992 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] Finished job 1159. 879 of 2231 steps (39%) done Select jobs to execute... [Fri Nov 3 10:34:15 2023] Finished job 329. 880 of 2231 steps (39%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-208.PRE.ext.gff. [Fri Nov 3 10:34:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-208.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-208.PRE.filtered.gff jobid: 1279 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-208.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-208.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-208.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-208.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-208.PRE.filtered.fasta jobid: 1838 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-208.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-208.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-208.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:15 2023] Finished job 1838. 881 of 2231 steps (39%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:15 2023] Finished job 1279. 882 of 2231 steps (40%) done [Fri Nov 3 10:34:23 2023] Finished job 992. 883 of 2231 steps (40%) done [Fri Nov 3 10:34:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9.PRE.gff, analyses/output/Amil-MirMachine/Mir-9.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9.PRE.unfiltered jobid: 991 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-21.PRE.CM output: analyses/output/Amil-MirMachine/Mir-21.PRE.result jobid: 332 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-21.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-21.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:23 2023] Finished job 991. 884 of 2231 steps (40%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9.PRE.filtered.gff jobid: 1610 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9.PRE.filtered.fasta jobid: 2169 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:23 2023] Finished job 2169. 885 of 2231 steps (40%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:24 2023] Finished job 1610. 886 of 2231 steps (40%) done [Fri Nov 3 10:34:27 2023] Finished job 108. 887 of 2231 steps (40%) done [Fri Nov 3 10:34:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-137.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-137.PRE.gff, analyses/output/Amil-MirMachine/Mir-137.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-137.PRE.unfiltered jobid: 107 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-137.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-137.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-137.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-105.PRE.CM output: analyses/output/Amil-MirMachine/Mir-105.PRE.result jobid: 32 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-105.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-105.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:28 2023] Finished job 107. 888 of 2231 steps (40%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-137.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-137.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-137.PRE.filtered.fasta jobid: 1727 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-137.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-137.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-137.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-137.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-137.PRE.filtered.gff jobid: 1168 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-137.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-137.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-137.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:28 2023] Finished job 1727. 889 of 2231 steps (40%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:28 2023] Finished job 1168. 890 of 2231 steps (40%) done [Fri Nov 3 10:34:29 2023] Finished job 332. 891 of 2231 steps (40%) done [Fri Nov 3 10:34:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-784.PRE.CM output: analyses/output/Amil-MirMachine/Mir-784.PRE.result jobid: 952 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-784.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-784.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-21.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-21.PRE.gff, analyses/output/Amil-MirMachine/Mir-21.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-21.PRE.unfiltered jobid: 331 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-21.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-21.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-21.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:29 2023] Finished job 331. 892 of 2231 steps (40%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-21.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-21.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-21.PRE.filtered.fasta jobid: 1839 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-21.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-21.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-21.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-21.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-21.PRE.filtered.gff jobid: 1280 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-21.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-21.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-21.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:29 2023] Finished job 1839. 893 of 2231 steps (40%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:29 2023] Finished job 1280. 894 of 2231 steps (40%) done [Fri Nov 3 10:34:32 2023] Finished job 32. 895 of 2231 steps (40%) done [Fri Nov 3 10:34:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-105.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-105.PRE.gff, analyses/output/Amil-MirMachine/Mir-105.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-105.PRE.unfiltered jobid: 31 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-105.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-105.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-105.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-132.PRE.CM output: analyses/output/Amil-MirMachine/Mir-132.PRE.result jobid: 92 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-132.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-132.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:33 2023] Finished job 31. 896 of 2231 steps (40%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-105.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-105.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-105.PRE.filtered.gff jobid: 1130 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-105.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-105.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-105.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-105.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-105.PRE.filtered.fasta jobid: 1689 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-105.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-105.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-105.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:33 2023] Finished job 1689. 897 of 2231 steps (40%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:33 2023] Finished job 1130. 898 of 2231 steps (40%) done [Fri Nov 3 10:34:39 2023] Finished job 952. 899 of 2231 steps (40%) done [Fri Nov 3 10:34:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-460.PRE.CM output: analyses/output/Amil-MirMachine/Mir-460.PRE.result jobid: 632 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-460.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-460.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-784.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-784.PRE.gff, analyses/output/Amil-MirMachine/Mir-784.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-784.PRE.unfiltered jobid: 951 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-784.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-784.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-784.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:39 2023] Finished job 951. 900 of 2231 steps (40%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-784.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-784.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-784.PRE.filtered.gff jobid: 1590 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-784.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-784.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-784.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-784.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-784.PRE.filtered.fasta jobid: 2149 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-784.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-784.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-784.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:39 2023] Finished job 2149. 901 of 2231 steps (40%) done Select jobs to execute... [Fri Nov 3 10:34:39 2023] Finished job 92. 902 of 2231 steps (40%) done [Fri Nov 3 10:34:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-132.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-132.PRE.gff, analyses/output/Amil-MirMachine/Mir-132.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-132.PRE.unfiltered jobid: 91 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-132.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-132.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-132.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7286.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7286.PRE.result jobid: 872 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7286.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7286.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:39 2023] Finished job 91. 903 of 2231 steps (40%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-132.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-132.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-132.PRE.filtered.fasta jobid: 1719 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-132.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-132.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-132.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-132.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-132.PRE.filtered.gff jobid: 1160 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-132.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-132.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-132.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:34:39 2023] Finished job 1719. 904 of 2231 steps (41%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:40 2023] Finished job 1590. 905 of 2231 steps (41%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:40 2023] Finished job 1160. 906 of 2231 steps (41%) done [Fri Nov 3 10:34:45 2023] Finished job 872. 907 of 2231 steps (41%) done [Fri Nov 3 10:34:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-425.PRE.CM output: analyses/output/Amil-MirMachine/Mir-425.PRE.result jobid: 594 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-425.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-425.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7286.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7286.PRE.gff, analyses/output/Amil-MirMachine/Mir-7286.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7286.PRE.unfiltered jobid: 871 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7286.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7286.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7286.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] Finished job 871. 908 of 2231 steps (41%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7286.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7286.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7286.PRE.filtered.gff jobid: 1550 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7286.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7286.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7286.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7286.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7286.PRE.filtered.fasta jobid: 2109 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7286.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7286.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7286.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] Finished job 2109. 909 of 2231 steps (41%) done Select jobs to execute... [Fri Nov 3 10:34:45 2023] Finished job 632. 910 of 2231 steps (41%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-460.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-460.PRE.gff, analyses/output/Amil-MirMachine/Mir-460.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-460.PRE.unfiltered jobid: 631 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-460.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-460.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-460.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-154.PRE.CM output: analyses/output/Amil-MirMachine/Mir-154.PRE.result jobid: 152 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-154.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-154.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] Finished job 1550. 911 of 2231 steps (41%) done Select jobs to execute... [Fri Nov 3 10:34:45 2023] Finished job 631. 912 of 2231 steps (41%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-460.PRE.ext.gff. [Fri Nov 3 10:34:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-460.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-460.PRE.filtered.gff jobid: 1430 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-460.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-460.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-460.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-460.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-460.PRE.filtered.fasta jobid: 1989 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-460.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-460.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-460.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:45 2023] Finished job 1989. 913 of 2231 steps (41%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:46 2023] Finished job 1430. 914 of 2231 steps (41%) done [Fri Nov 3 10:34:49 2023] Finished job 594. 915 of 2231 steps (41%) done [Fri Nov 3 10:34:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-425.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-425.PRE.gff, analyses/output/Amil-MirMachine/Mir-425.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-425.PRE.unfiltered jobid: 593 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-425.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-425.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-425.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-337.PRE.CM output: analyses/output/Amil-MirMachine/Mir-337.PRE.result jobid: 534 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-337.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-337.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:49 2023] Finished job 593. 916 of 2231 steps (41%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-425.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-425.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-425.PRE.filtered.fasta jobid: 1970 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-425.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-425.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-425.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-425.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-425.PRE.filtered.gff jobid: 1411 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-425.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-425.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-425.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:49 2023] Finished job 1970. 917 of 2231 steps (41%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:49 2023] Finished job 1411. 918 of 2231 steps (41%) done [Fri Nov 3 10:34:52 2023] Finished job 152. 919 of 2231 steps (41%) done [Fri Nov 3 10:34:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-154.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-154.PRE.gff, analyses/output/Amil-MirMachine/Mir-154.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-154.PRE.unfiltered jobid: 151 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-154.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-154.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-154.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1911.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1911.PRE.result jobid: 212 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1911.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1911.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:52 2023] Finished job 151. 920 of 2231 steps (41%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-154.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-154.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-154.PRE.filtered.gff jobid: 1190 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-154.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-154.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-154.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-154.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-154.PRE.filtered.fasta jobid: 1749 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-154.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-154.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-154.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:52 2023] Finished job 1749. 921 of 2231 steps (41%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:53 2023] Finished job 1190. 922 of 2231 steps (41%) done [Fri Nov 3 10:34:54 2023] Finished job 534. 923 of 2231 steps (41%) done [Fri Nov 3 10:34:54 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-337.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-337.PRE.gff, analyses/output/Amil-MirMachine/Mir-337.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-337.PRE.unfiltered jobid: 533 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-337.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-337.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-337.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:54 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-202.PRE.CM output: analyses/output/Amil-MirMachine/Mir-202.PRE.result jobid: 294 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-202.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-202.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:55 2023] Finished job 533. 924 of 2231 steps (41%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-337.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-337.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-337.PRE.filtered.gff jobid: 1381 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-337.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-337.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-337.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-337.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-337.PRE.filtered.fasta jobid: 1940 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-337.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-337.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-337.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:55 2023] Finished job 1940. 925 of 2231 steps (41%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:55 2023] Finished job 1381. 926 of 2231 steps (42%) done [Fri Nov 3 10:34:56 2023] Finished job 212. 927 of 2231 steps (42%) done [Fri Nov 3 10:34:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1911.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1911.PRE.gff, analyses/output/Amil-MirMachine/Mir-1911.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1911.PRE.unfiltered jobid: 211 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1911.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1911.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1911.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1995.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1995.PRE.result jobid: 250 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1995.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1995.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:34:56 2023] Finished job 211. 928 of 2231 steps (42%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1911.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:34:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1911.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1911.PRE.filtered.fasta jobid: 1779 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1911.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1911.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1911.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1911.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1911.PRE.filtered.gff jobid: 1220 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1911.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1911.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1911.PRE resources: tmpdir=/tmp [Fri Nov 3 10:34:56 2023] Finished job 1779. 929 of 2231 steps (42%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:34:57 2023] Finished job 1220. 930 of 2231 steps (42%) done [Fri Nov 3 10:35:02 2023] Finished job 294. 931 of 2231 steps (42%) done [Fri Nov 3 10:35:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-202.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-202.PRE.gff, analyses/output/Amil-MirMachine/Mir-202.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-202.PRE.unfiltered jobid: 293 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-202.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-202.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-202.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7397.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7397.PRE.result jobid: 932 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7397.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7397.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:03 2023] Finished job 293. 932 of 2231 steps (42%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-202.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-202.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-202.PRE.filtered.gff jobid: 1261 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-202.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-202.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-202.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-202.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-202.PRE.filtered.fasta jobid: 1820 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-202.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-202.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-202.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:03 2023] Finished job 1820. 933 of 2231 steps (42%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:03 2023] Finished job 1261. 934 of 2231 steps (42%) done [Fri Nov 3 10:35:04 2023] Finished job 250. 935 of 2231 steps (42%) done [Fri Nov 3 10:35:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-550.PRE.CM output: analyses/output/Amil-MirMachine/Mir-550.PRE.result jobid: 752 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-550.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-550.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1995.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1995.PRE.gff, analyses/output/Amil-MirMachine/Mir-1995.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1995.PRE.unfiltered jobid: 249 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1995.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1995.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1995.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:04 2023] Finished job 249. 936 of 2231 steps (42%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1995.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1995.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1995.PRE.filtered.gff jobid: 1239 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1995.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1995.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1995.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1995.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1995.PRE.filtered.fasta jobid: 1798 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1995.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1995.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1995.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:04 2023] Finished job 1798. 937 of 2231 steps (42%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:04 2023] Finished job 1239. 938 of 2231 steps (42%) done [Fri Nov 3 10:35:08 2023] Finished job 752. 939 of 2231 steps (42%) done [Fri Nov 3 10:35:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-550.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-550.PRE.gff, analyses/output/Amil-MirMachine/Mir-550.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-550.PRE.unfiltered jobid: 751 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-550.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-550.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-550.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3099.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3099.PRE.result jobid: 490 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3099.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3099.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:08 2023] Finished job 751. 940 of 2231 steps (42%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-550.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-550.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-550.PRE.filtered.gff jobid: 1490 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-550.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-550.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-550.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-550.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-550.PRE.filtered.fasta jobid: 2049 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-550.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-550.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-550.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:08 2023] Finished job 2049. 941 of 2231 steps (42%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:08 2023] Finished job 1490. 942 of 2231 steps (42%) done [Fri Nov 3 10:35:10 2023] Finished job 932. 943 of 2231 steps (42%) done [Fri Nov 3 10:35:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7397.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7397.PRE.gff, analyses/output/Amil-MirMachine/Mir-7397.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7397.PRE.unfiltered jobid: 931 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7397.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7397.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7397.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-350.PRE.CM output: analyses/output/Amil-MirMachine/Mir-350.PRE.result jobid: 550 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-350.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-350.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:10 2023] Finished job 931. 944 of 2231 steps (42%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7397.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7397.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7397.PRE.filtered.fasta jobid: 2139 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7397.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7397.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7397.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7397.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7397.PRE.filtered.gff jobid: 1580 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7397.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7397.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7397.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:10 2023] Finished job 2139. 945 of 2231 steps (42%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:11 2023] Finished job 1580. 946 of 2231 steps (42%) done [Fri Nov 3 10:35:11 2023] Finished job 490. 947 of 2231 steps (42%) done [Fri Nov 3 10:35:11 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3099.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3099.PRE.gff, analyses/output/Amil-MirMachine/Mir-3099.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3099.PRE.unfiltered jobid: 489 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3099.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3099.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3099.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:11 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-551.PRE.CM output: analyses/output/Amil-MirMachine/Mir-551.PRE.result jobid: 754 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-551.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-551.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:11 2023] Finished job 489. 948 of 2231 steps (42%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3099.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3099.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3099.PRE.filtered.fasta jobid: 1918 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3099.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3099.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3099.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3099.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3099.PRE.filtered.gff jobid: 1359 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3099.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3099.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3099.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:11 2023] Finished job 1918. 949 of 2231 steps (43%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:12 2023] Finished job 1359. 950 of 2231 steps (43%) done [Fri Nov 3 10:35:16 2023] Finished job 550. 951 of 2231 steps (43%) done [Fri Nov 3 10:35:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-350.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-350.PRE.gff, analyses/output/Amil-MirMachine/Mir-350.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-350.PRE.unfiltered jobid: 549 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-350.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-350.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-350.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-210.PRE.CM output: analyses/output/Amil-MirMachine/Mir-210.PRE.result jobid: 334 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-210.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-210.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:16 2023] Finished job 549. 952 of 2231 steps (43%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-350.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-350.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-350.PRE.filtered.gff jobid: 1389 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-350.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-350.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-350.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-350.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-350.PRE.filtered.fasta jobid: 1948 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-350.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-350.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-350.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:16 2023] Finished job 1948. 953 of 2231 steps (43%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:16 2023] Finished job 1389. 954 of 2231 steps (43%) done [Fri Nov 3 10:35:17 2023] Finished job 754. 955 of 2231 steps (43%) done [Fri Nov 3 10:35:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-551.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-551.PRE.gff, analyses/output/Amil-MirMachine/Mir-551.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-551.PRE.unfiltered jobid: 753 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-551.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-551.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-551.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1175.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1175.PRE.result jobid: 34 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1175.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1175.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:17 2023] Finished job 753. 956 of 2231 steps (43%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-551.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-551.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-551.PRE.filtered.gff jobid: 1491 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-551.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-551.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-551.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-551.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-551.PRE.filtered.fasta jobid: 2050 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-551.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-551.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-551.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:17 2023] Finished job 2050. 957 of 2231 steps (43%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:17 2023] Finished job 1491. 958 of 2231 steps (43%) done [Fri Nov 3 10:35:21 2023] Finished job 334. 959 of 2231 steps (43%) done [Fri Nov 3 10:35:21 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-210.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-210.PRE.gff, analyses/output/Amil-MirMachine/Mir-210.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-210.PRE.unfiltered jobid: 333 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-210.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-210.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-210.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:21 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2501.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2501.PRE.result jobid: 394 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2501.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2501.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:21 2023] Finished job 333. 960 of 2231 steps (43%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-210.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:21 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-210.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-210.PRE.filtered.fasta jobid: 1840 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-210.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-210.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-210.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:21 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-210.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-210.PRE.filtered.gff jobid: 1281 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-210.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-210.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-210.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:21 2023] Finished job 1840. 961 of 2231 steps (43%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:21 2023] Finished job 1281. 962 of 2231 steps (43%) done [Fri Nov 3 10:35:25 2023] Finished job 34. 963 of 2231 steps (43%) done [Fri Nov 3 10:35:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1175.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1175.PRE.gff, analyses/output/Amil-MirMachine/Mir-1175.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1175.PRE.unfiltered jobid: 33 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1175.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1175.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1175.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1323.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1323.PRE.result jobid: 94 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1323.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1323.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:25 2023] Finished job 33. 964 of 2231 steps (43%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1175.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1175.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1175.PRE.filtered.gff jobid: 1131 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1175.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1175.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1175.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1175.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1175.PRE.filtered.fasta jobid: 1690 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1175.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1175.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1175.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:25 2023] Finished job 1690. 965 of 2231 steps (43%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:25 2023] Finished job 1131. 966 of 2231 steps (43%) done [Fri Nov 3 10:35:26 2023] Finished job 394. 967 of 2231 steps (43%) done [Fri Nov 3 10:35:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2501.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2501.PRE.gff, analyses/output/Amil-MirMachine/Mir-2501.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2501.PRE.unfiltered jobid: 393 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2501.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2501.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2501.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4677.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4677.PRE.result jobid: 634 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4677.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4677.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:26 2023] Finished job 393. 968 of 2231 steps (43%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2501.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2501.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2501.PRE.filtered.gff jobid: 1311 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2501.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2501.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2501.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2501.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2501.PRE.filtered.fasta jobid: 1870 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2501.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2501.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2501.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:26 2023] Finished job 1870. 969 of 2231 steps (43%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:27 2023] Finished job 1311. 970 of 2231 steps (43%) done [Fri Nov 3 10:35:30 2023] Finished job 94. 971 of 2231 steps (44%) done [Fri Nov 3 10:35:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1323.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1323.PRE.gff, analyses/output/Amil-MirMachine/Mir-1323.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1323.PRE.unfiltered jobid: 93 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1323.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1323.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1323.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-90.PRE.CM output: analyses/output/Amil-MirMachine/Mir-90.PRE.result jobid: 994 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-90.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-90.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] Finished job 93. 972 of 2231 steps (44%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1323.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1323.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1323.PRE.filtered.fasta jobid: 1720 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1323.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1323.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1323.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1323.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1323.PRE.filtered.gff jobid: 1161 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1323.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1323.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1323.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] Finished job 1720. 973 of 2231 steps (44%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:30 2023] Finished job 1161. 974 of 2231 steps (44%) done [Fri Nov 3 10:35:30 2023] Finished job 634. 975 of 2231 steps (44%) done [Fri Nov 3 10:35:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4677.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4677.PRE.gff, analyses/output/Amil-MirMachine/Mir-4677.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4677.PRE.unfiltered jobid: 633 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4677.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4677.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4677.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-729.PRE.CM output: analyses/output/Amil-MirMachine/Mir-729.PRE.result jobid: 874 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-729.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-729.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] Finished job 633. 976 of 2231 steps (44%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4677.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4677.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4677.PRE.filtered.gff jobid: 1431 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4677.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4677.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4677.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4677.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4677.PRE.filtered.fasta jobid: 1990 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4677.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4677.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4677.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:30 2023] Finished job 1990. 977 of 2231 steps (44%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:31 2023] Finished job 1431. 978 of 2231 steps (44%) done [Fri Nov 3 10:35:36 2023] Finished job 874. 979 of 2231 steps (44%) done [Fri Nov 3 10:35:36 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-729.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-729.PRE.gff, analyses/output/Amil-MirMachine/Mir-729.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-729.PRE.unfiltered jobid: 873 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-729.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-729.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-729.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:36 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-589.PRE.CM output: analyses/output/Amil-MirMachine/Mir-589.PRE.result jobid: 770 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-589.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-589.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:36 2023] Finished job 873. 980 of 2231 steps (44%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-729.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:36 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-729.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-729.PRE.filtered.gff jobid: 1551 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-729.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-729.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-729.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:36 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-729.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-729.PRE.filtered.fasta jobid: 2110 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-729.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-729.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-729.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:36 2023] Finished job 2110. 981 of 2231 steps (44%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:37 2023] Finished job 1551. 982 of 2231 steps (44%) done [Fri Nov 3 10:35:40 2023] Finished job 994. 983 of 2231 steps (44%) done [Fri Nov 3 10:35:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-90.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-90.PRE.gff, analyses/output/Amil-MirMachine/Mir-90.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-90.PRE.unfiltered jobid: 993 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-90.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-90.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-90.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1540.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1540.PRE.result jobid: 154 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1540.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1540.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] Finished job 993. 984 of 2231 steps (44%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-90.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-90.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-90.PRE.filtered.gff jobid: 1611 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-90.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-90.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-90.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-90.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-90.PRE.filtered.fasta jobid: 2170 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-90.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-90.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-90.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] Finished job 770. 985 of 2231 steps (44%) done Select jobs to execute... [Fri Nov 3 10:35:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-589.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-589.PRE.gff, analyses/output/Amil-MirMachine/Mir-589.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-589.PRE.unfiltered jobid: 769 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-589.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-589.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-589.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1912.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1912.PRE.result jobid: 214 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1912.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1912.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] Finished job 2170. 986 of 2231 steps (44%) done Select jobs to execute... [Fri Nov 3 10:35:40 2023] Finished job 769. 987 of 2231 steps (44%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-589.PRE.ext.gff. [Fri Nov 3 10:35:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-589.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-589.PRE.filtered.gff jobid: 1499 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-589.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-589.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-589.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-589.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-589.PRE.filtered.fasta jobid: 2058 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-589.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-589.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-589.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:40 2023] Finished job 2058. 988 of 2231 steps (44%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:40 2023] Finished job 1611. 989 of 2231 steps (44%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:40 2023] Finished job 1499. 990 of 2231 steps (44%) done [Fri Nov 3 10:35:42 2023] Finished job 154. 991 of 2231 steps (44%) done [Fri Nov 3 10:35:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3049.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3049.PRE.result jobid: 474 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3049.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3049.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1540.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1540.PRE.gff, analyses/output/Amil-MirMachine/Mir-1540.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1540.PRE.unfiltered jobid: 153 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1540.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1540.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:43 2023] Finished job 153. 992 of 2231 steps (44%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1540.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1540.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1540.PRE.filtered.gff jobid: 1191 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1540.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1540.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1540.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1540.PRE.filtered.fasta jobid: 1750 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1540.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1540.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:43 2023] Finished job 1750. 993 of 2231 steps (45%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:43 2023] Finished job 1191. 994 of 2231 steps (45%) done [Fri Nov 3 10:35:47 2023] Finished job 474. 995 of 2231 steps (45%) done [Fri Nov 3 10:35:47 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7292.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7292.PRE.result jobid: 876 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7292.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7292.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:47 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3049.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3049.PRE.gff, analyses/output/Amil-MirMachine/Mir-3049.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3049.PRE.unfiltered jobid: 473 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3049.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3049.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3049.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:47 2023] Finished job 473. 996 of 2231 steps (45%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3049.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:47 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3049.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3049.PRE.filtered.gff jobid: 1351 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3049.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3049.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3049.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:47 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3049.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3049.PRE.filtered.fasta jobid: 1910 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3049.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3049.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3049.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:47 2023] Finished job 1910. 997 of 2231 steps (45%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:48 2023] Finished job 1351. 998 of 2231 steps (45%) done [Fri Nov 3 10:35:50 2023] Finished job 214. 999 of 2231 steps (45%) done [Fri Nov 3 10:35:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2017.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2017.PRE.result jobid: 288 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2017.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2017.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1912.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1912.PRE.gff, analyses/output/Amil-MirMachine/Mir-1912.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1912.PRE.unfiltered jobid: 213 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1912.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1912.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1912.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:50 2023] Finished job 213. 1000 of 2231 steps (45%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1912.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1912.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1912.PRE.filtered.fasta jobid: 1780 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1912.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1912.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1912.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1912.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1912.PRE.filtered.gff jobid: 1221 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1912.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1912.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1912.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:51 2023] Finished job 1780. 1001 of 2231 steps (45%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:51 2023] Finished job 1221. 1002 of 2231 steps (45%) done [Fri Nov 3 10:35:52 2023] Finished job 876. 1003 of 2231 steps (45%) done [Fri Nov 3 10:35:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3934.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3934.PRE.result jobid: 588 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3934.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3934.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7292.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7292.PRE.gff, analyses/output/Amil-MirMachine/Mir-7292.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7292.PRE.unfiltered jobid: 875 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7292.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-7292.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7292.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:52 2023] Finished job 875. 1004 of 2231 steps (45%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7292.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7292.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7292.PRE.filtered.fasta jobid: 2111 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7292.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7292.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7292.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7292.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7292.PRE.filtered.gff jobid: 1552 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7292.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7292.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7292.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:52 2023] Finished job 2111. 1005 of 2231 steps (45%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:52 2023] Finished job 1552. 1006 of 2231 steps (45%) done [Fri Nov 3 10:35:55 2023] Finished job 288. 1007 of 2231 steps (45%) done [Fri Nov 3 10:35:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2017.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2017.PRE.gff, analyses/output/Amil-MirMachine/Mir-2017.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2017.PRE.unfiltered jobid: 287 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2017.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2017.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2017.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2.PRE.result jobid: 258 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:55 2023] Finished job 287. 1008 of 2231 steps (45%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2017.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2017.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2017.PRE.filtered.gff jobid: 1258 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2017.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2017.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2017.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2017.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2017.PRE.filtered.fasta jobid: 1817 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2017.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2017.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2017.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:55 2023] Finished job 1817. 1009 of 2231 steps (45%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:56 2023] Finished job 1258. 1010 of 2231 steps (45%) done [Fri Nov 3 10:35:56 2023] Finished job 588. 1011 of 2231 steps (45%) done [Fri Nov 3 10:35:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3934.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3934.PRE.gff, analyses/output/Amil-MirMachine/Mir-3934.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3934.PRE.unfiltered jobid: 587 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3934.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3934.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3934.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3140.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3140.PRE.result jobid: 498 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3140.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3140.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:35:56 2023] Finished job 587. 1012 of 2231 steps (45%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3934.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:35:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3934.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3934.PRE.filtered.fasta jobid: 1967 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3934.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3934.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3934.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3934.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3934.PRE.filtered.gff jobid: 1408 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3934.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3934.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3934.PRE resources: tmpdir=/tmp [Fri Nov 3 10:35:56 2023] Finished job 1967. 1013 of 2231 steps (45%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:35:57 2023] Finished job 1408. 1014 of 2231 steps (45%) done [Fri Nov 3 10:36:05 2023] Finished job 258. 1015 of 2231 steps (45%) done [Fri Nov 3 10:36:05 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2.PRE.gff, analyses/output/Amil-MirMachine/Mir-2.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2.PRE.unfiltered jobid: 257 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:05 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2765.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2765.PRE.result jobid: 438 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2765.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2765.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:05 2023] Finished job 257. 1016 of 2231 steps (46%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:05 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2.PRE.filtered.gff jobid: 1243 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:05 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2.PRE.filtered.fasta jobid: 1802 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:05 2023] Finished job 1802. 1017 of 2231 steps (46%) done Select jobs to execute... [Fri Nov 3 10:36:05 2023] Finished job 498. 1018 of 2231 steps (46%) done [Fri Nov 3 10:36:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3140.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3140.PRE.gff, analyses/output/Amil-MirMachine/Mir-3140.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3140.PRE.unfiltered jobid: 497 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3140.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3140.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3140.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4862.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4862.PRE.result jobid: 678 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4862.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4862.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:06 2023] Finished job 497. 1019 of 2231 steps (46%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3140.PRE.ext.gff. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:36:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3140.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3140.PRE.filtered.gff jobid: 1363 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3140.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3140.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3140.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3140.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3140.PRE.filtered.fasta jobid: 1922 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3140.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3140.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3140.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:06 2023] Finished job 1922. 1020 of 2231 steps (46%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:06 2023] Finished job 1243. 1021 of 2231 steps (46%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:06 2023] Finished job 1363. 1022 of 2231 steps (46%) done [Fri Nov 3 10:36:09 2023] Finished job 438. 1023 of 2231 steps (46%) done [Fri Nov 3 10:36:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2765.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2765.PRE.gff, analyses/output/Amil-MirMachine/Mir-2765.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2765.PRE.unfiltered jobid: 437 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2765.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2765.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2765.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-6529.PRE.CM output: analyses/output/Amil-MirMachine/Mir-6529.PRE.result jobid: 798 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6529.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-6529.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:09 2023] Finished job 437. 1024 of 2231 steps (46%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2765.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2765.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2765.PRE.filtered.fasta jobid: 1892 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2765.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2765.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2765.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2765.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2765.PRE.filtered.gff jobid: 1333 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2765.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2765.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2765.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:09 2023] Finished job 1892. 1025 of 2231 steps (46%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:10 2023] Finished job 1333. 1026 of 2231 steps (46%) done [Fri Nov 3 10:36:10 2023] Finished job 678. 1027 of 2231 steps (46%) done [Fri Nov 3 10:36:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-700.PRE.CM output: analyses/output/Amil-MirMachine/Mir-700.PRE.result jobid: 828 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-700.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-700.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4862.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4862.PRE.gff, analyses/output/Amil-MirMachine/Mir-4862.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4862.PRE.unfiltered jobid: 677 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4862.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4862.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4862.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:10 2023] Finished job 677. 1028 of 2231 steps (46%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4862.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4862.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4862.PRE.filtered.fasta jobid: 2012 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4862.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4862.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4862.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4862.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4862.PRE.filtered.gff jobid: 1453 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4862.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4862.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4862.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:10 2023] Finished job 2012. 1029 of 2231 steps (46%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:11 2023] Finished job 1453. 1030 of 2231 steps (46%) done [Fri Nov 3 10:36:13 2023] Finished job 798. 1031 of 2231 steps (46%) done [Fri Nov 3 10:36:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9369.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9369.PRE.result jobid: 1008 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9369.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9369.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-6529.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-6529.PRE.gff, analyses/output/Amil-MirMachine/Mir-6529.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-6529.PRE.unfiltered jobid: 797 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6529.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-6529.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-6529.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:13 2023] Finished job 797. 1032 of 2231 steps (46%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-6529.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-6529.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-6529.PRE.filtered.fasta jobid: 2072 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6529.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-6529.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-6529.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-6529.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-6529.PRE.filtered.gff jobid: 1513 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6529.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-6529.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-6529.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:13 2023] Finished job 2072. 1033 of 2231 steps (46%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:13 2023] Finished job 1513. 1034 of 2231 steps (46%) done [Fri Nov 3 10:36:14 2023] Finished job 828. 1035 of 2231 steps (46%) done [Fri Nov 3 10:36:14 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-700.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-700.PRE.gff, analyses/output/Amil-MirMachine/Mir-700.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-700.PRE.unfiltered jobid: 827 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-700.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-700.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-700.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:14 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4825.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4825.PRE.result jobid: 648 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4825.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4825.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:14 2023] Finished job 827. 1036 of 2231 steps (46%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-700.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-700.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-700.PRE.filtered.fasta jobid: 2087 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-700.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-700.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-700.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-700.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-700.PRE.filtered.gff jobid: 1528 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-700.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-700.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-700.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:14 2023] Finished job 2087. 1037 of 2231 steps (46%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:14 2023] Finished job 1528. 1038 of 2231 steps (47%) done [Fri Nov 3 10:36:19 2023] Finished job 1008. 1039 of 2231 steps (47%) done [Fri Nov 3 10:36:19 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9369.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9369.PRE.gff, analyses/output/Amil-MirMachine/Mir-9369.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9369.PRE.unfiltered jobid: 1007 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9369.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9369.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9369.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:19 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7319.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7319.PRE.result jobid: 888 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7319.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7319.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:19 2023] Finished job 1007. 1040 of 2231 steps (47%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9369.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:19 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9369.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9369.PRE.filtered.gff jobid: 1618 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9369.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9369.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9369.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:19 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9369.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9369.PRE.filtered.fasta jobid: 2177 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9369.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9369.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9369.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:19 2023] Finished job 2177. 1041 of 2231 steps (47%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:19 2023] Finished job 1618. 1042 of 2231 steps (47%) done [Fri Nov 3 10:36:20 2023] Finished job 648. 1043 of 2231 steps (47%) done [Fri Nov 3 10:36:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4825.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4825.PRE.gff, analyses/output/Amil-MirMachine/Mir-4825.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4825.PRE.unfiltered jobid: 647 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4825.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4825.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4825.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-584.PRE.CM output: analyses/output/Amil-MirMachine/Mir-584.PRE.result jobid: 768 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-584.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-584.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:20 2023] Finished job 647. 1044 of 2231 steps (47%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4825.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4825.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4825.PRE.filtered.gff jobid: 1438 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4825.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4825.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4825.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4825.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4825.PRE.filtered.fasta jobid: 1997 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4825.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4825.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4825.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:20 2023] Finished job 1997. 1045 of 2231 steps (47%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:20 2023] Finished job 1438. 1046 of 2231 steps (47%) done [Fri Nov 3 10:36:23 2023] Finished job 888. 1047 of 2231 steps (47%) done [Fri Nov 3 10:36:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7319.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7319.PRE.gff, analyses/output/Amil-MirMachine/Mir-7319.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7319.PRE.unfiltered jobid: 887 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7319.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7319.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7319.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1552.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1552.PRE.result jobid: 168 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1552.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1552.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] Finished job 768. 1048 of 2231 steps (47%) done Select jobs to execute... [Fri Nov 3 10:36:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-584.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-584.PRE.gff, analyses/output/Amil-MirMachine/Mir-584.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-584.PRE.unfiltered jobid: 767 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-584.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-584.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-584.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12316.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12316.PRE.result jobid: 48 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12316.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12316.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] Finished job 887. 1049 of 2231 steps (47%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7319.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7319.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7319.PRE.filtered.gff jobid: 1558 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7319.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7319.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7319.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7319.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7319.PRE.filtered.fasta jobid: 2117 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7319.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7319.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7319.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] Finished job 767. 1050 of 2231 steps (47%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-584.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-584.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-584.PRE.filtered.gff jobid: 1498 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-584.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-584.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-584.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-584.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-584.PRE.filtered.fasta jobid: 2057 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-584.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-584.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-584.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:24 2023] Finished job 2117. 1051 of 2231 steps (47%) done Select jobs to execute... [Fri Nov 3 10:36:24 2023] Finished job 2057. 1052 of 2231 steps (47%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:24 2023] Finished job 1558. 1053 of 2231 steps (47%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:24 2023] Finished job 1498. 1054 of 2231 steps (47%) done [Fri Nov 3 10:36:27 2023] Finished job 168. 1055 of 2231 steps (47%) done [Fri Nov 3 10:36:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1552.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1552.PRE.gff, analyses/output/Amil-MirMachine/Mir-1552.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1552.PRE.unfiltered jobid: 167 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1552.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1552.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1552.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-197.PRE.CM output: analyses/output/Amil-MirMachine/Mir-197.PRE.result jobid: 228 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-197.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-197.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:27 2023] Finished job 167. 1056 of 2231 steps (47%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1552.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1552.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1552.PRE.filtered.gff jobid: 1198 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1552.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1552.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1552.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1552.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1552.PRE.filtered.fasta jobid: 1757 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1552.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1552.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1552.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:28 2023] Finished job 1757. 1057 of 2231 steps (47%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:28 2023] Finished job 1198. 1058 of 2231 steps (47%) done [Fri Nov 3 10:36:28 2023] Finished job 48. 1059 of 2231 steps (47%) done [Fri Nov 3 10:36:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12316.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12316.PRE.gff, analyses/output/Amil-MirMachine/Mir-12316.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12316.PRE.unfiltered jobid: 47 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12316.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12316.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12316.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2184.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2184.PRE.result jobid: 348 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2184.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2184.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:28 2023] Finished job 47. 1060 of 2231 steps (48%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12316.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12316.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12316.PRE.filtered.gff jobid: 1138 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12316.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12316.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12316.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12316.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12316.PRE.filtered.fasta jobid: 1697 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12316.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12316.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12316.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:28 2023] Finished job 1697. 1061 of 2231 steps (48%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:29 2023] Finished job 1138. 1062 of 2231 steps (48%) done [Fri Nov 3 10:36:32 2023] Finished job 228. 1063 of 2231 steps (48%) done [Fri Nov 3 10:36:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-197.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-197.PRE.gff, analyses/output/Amil-MirMachine/Mir-197.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-197.PRE.unfiltered jobid: 227 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-197.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-197.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-197.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-77.PRE.CM output: analyses/output/Amil-MirMachine/Mir-77.PRE.result jobid: 948 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-77.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-77.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:32 2023] Finished job 227. 1064 of 2231 steps (48%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-197.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-197.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-197.PRE.filtered.fasta jobid: 1787 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-197.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-197.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-197.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-197.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-197.PRE.filtered.gff jobid: 1228 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-197.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-197.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-197.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:32 2023] Finished job 1787. 1065 of 2231 steps (48%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:32 2023] Finished job 1228. 1066 of 2231 steps (48%) done [Fri Nov 3 10:36:34 2023] Finished job 348. 1067 of 2231 steps (48%) done [Fri Nov 3 10:36:35 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2184.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2184.PRE.gff, analyses/output/Amil-MirMachine/Mir-2184.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2184.PRE.unfiltered jobid: 347 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2184.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2184.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2184.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:35 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4887.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4887.PRE.result jobid: 708 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4887.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4887.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:35 2023] Finished job 347. 1068 of 2231 steps (48%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2184.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2184.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2184.PRE.filtered.fasta jobid: 1847 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2184.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2184.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2184.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2184.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2184.PRE.filtered.gff jobid: 1288 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2184.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2184.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2184.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:35 2023] Finished job 1847. 1069 of 2231 steps (48%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:35 2023] Finished job 1288. 1070 of 2231 steps (48%) done [Fri Nov 3 10:36:39 2023] Finished job 948. 1071 of 2231 steps (48%) done [Fri Nov 3 10:36:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-77.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-77.PRE.gff, analyses/output/Amil-MirMachine/Mir-77.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-77.PRE.unfiltered jobid: 947 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-77.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-77.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-77.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2584.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2584.PRE.result jobid: 408 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2584.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2584.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:39 2023] Finished job 947. 1072 of 2231 steps (48%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-77.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-77.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-77.PRE.filtered.fasta jobid: 2147 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-77.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-77.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-77.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-77.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-77.PRE.filtered.gff jobid: 1588 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-77.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-77.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-77.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:39 2023] Finished job 2147. 1073 of 2231 steps (48%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:39 2023] Finished job 1588. 1074 of 2231 steps (48%) done [Fri Nov 3 10:36:40 2023] Finished job 708. 1075 of 2231 steps (48%) done [Fri Nov 3 10:36:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4887.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4887.PRE.gff, analyses/output/Amil-MirMachine/Mir-4887.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4887.PRE.unfiltered jobid: 707 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4887.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4887.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4887.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-577.PRE.CM output: analyses/output/Amil-MirMachine/Mir-577.PRE.result jobid: 762 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-577.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-577.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:40 2023] Finished job 707. 1076 of 2231 steps (48%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4887.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4887.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4887.PRE.filtered.fasta jobid: 2027 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4887.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4887.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4887.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4887.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4887.PRE.filtered.gff jobid: 1468 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4887.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4887.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4887.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:40 2023] Finished job 2027. 1077 of 2231 steps (48%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:41 2023] Finished job 1468. 1078 of 2231 steps (48%) done [Fri Nov 3 10:36:45 2023] Finished job 762. 1079 of 2231 steps (48%) done [Fri Nov 3 10:36:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-592.PRE.CM output: analyses/output/Amil-MirMachine/Mir-592.PRE.result jobid: 774 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-592.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-592.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-577.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-577.PRE.gff, analyses/output/Amil-MirMachine/Mir-577.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-577.PRE.unfiltered jobid: 761 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-577.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-577.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-577.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:45 2023] Finished job 761. 1080 of 2231 steps (48%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-577.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-577.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-577.PRE.filtered.fasta jobid: 2054 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-577.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-577.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-577.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-577.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-577.PRE.filtered.gff jobid: 1495 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-577.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-577.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-577.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:45 2023] Finished job 2054. 1081 of 2231 steps (48%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:45 2023] Finished job 1495. 1082 of 2231 steps (48%) done [Fri Nov 3 10:36:49 2023] Finished job 774. 1083 of 2231 steps (49%) done [Fri Nov 3 10:36:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-592.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-592.PRE.gff, analyses/output/Amil-MirMachine/Mir-592.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-592.PRE.unfiltered jobid: 773 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-592.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-592.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-592.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9703.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9703.PRE.result jobid: 1068 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9703.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9703.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:49 2023] Finished job 773. 1084 of 2231 steps (49%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-592.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-592.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-592.PRE.filtered.gff jobid: 1501 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-592.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-592.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-592.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-592.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-592.PRE.filtered.fasta jobid: 2060 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-592.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-592.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-592.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:50 2023] Finished job 408. 1085 of 2231 steps (49%) done Select jobs to execute... [Fri Nov 3 10:36:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2584.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2584.PRE.gff, analyses/output/Amil-MirMachine/Mir-2584.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2584.PRE.unfiltered jobid: 407 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2584.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2584.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2584.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-340.PRE.CM output: analyses/output/Amil-MirMachine/Mir-340.PRE.result jobid: 542 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-340.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-340.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:50 2023] Finished job 2060. 1086 of 2231 steps (49%) done Select jobs to execute... [Fri Nov 3 10:36:50 2023] Finished job 407. 1087 of 2231 steps (49%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2584.PRE.ext.gff. [Fri Nov 3 10:36:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2584.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2584.PRE.filtered.gff jobid: 1318 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2584.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2584.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2584.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2584.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2584.PRE.filtered.fasta jobid: 1877 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2584.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2584.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2584.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:50 2023] Finished job 1877. 1088 of 2231 steps (49%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:50 2023] Finished job 1501. 1089 of 2231 steps (49%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:50 2023] Finished job 1318. 1090 of 2231 steps (49%) done [Fri Nov 3 10:36:53 2023] Finished job 1068. 1091 of 2231 steps (49%) done [Fri Nov 3 10:36:53 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9703.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9703.PRE.gff, analyses/output/Amil-MirMachine/Mir-9703.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9703.PRE.unfiltered jobid: 1067 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9703.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9703.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9703.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:53 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2691.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2691.PRE.result jobid: 422 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2691.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2691.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:53 2023] Finished job 1067. 1092 of 2231 steps (49%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9703.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:54 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9703.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9703.PRE.filtered.fasta jobid: 2207 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9703.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9703.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9703.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:54 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9703.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9703.PRE.filtered.gff jobid: 1648 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9703.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9703.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9703.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:54 2023] Finished job 2207. 1093 of 2231 steps (49%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:54 2023] Finished job 1648. 1094 of 2231 steps (49%) done [Fri Nov 3 10:36:58 2023] Finished job 542. 1095 of 2231 steps (49%) done [Fri Nov 3 10:36:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-340.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-340.PRE.gff, analyses/output/Amil-MirMachine/Mir-340.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-340.PRE.unfiltered jobid: 541 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-340.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-340.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-340.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3068.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3068.PRE.result jobid: 482 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3068.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3068.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:36:58 2023] Finished job 541. 1096 of 2231 steps (49%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-340.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:36:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-340.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-340.PRE.filtered.gff jobid: 1385 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-340.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-340.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-340.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-340.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-340.PRE.filtered.fasta jobid: 1944 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-340.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-340.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-340.PRE resources: tmpdir=/tmp [Fri Nov 3 10:36:58 2023] Finished job 1944. 1097 of 2231 steps (49%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:36:59 2023] Finished job 1385. 1098 of 2231 steps (49%) done [Fri Nov 3 10:37:03 2023] Finished job 482. 1099 of 2231 steps (49%) done [Fri Nov 3 10:37:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3068.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3068.PRE.gff, analyses/output/Amil-MirMachine/Mir-3068.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3068.PRE.unfiltered jobid: 481 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3068.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3068.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3068.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9851.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9851.PRE.result jobid: 1098 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9851.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9851.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:03 2023] Finished job 481. 1100 of 2231 steps (49%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3068.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3068.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3068.PRE.filtered.fasta jobid: 1914 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3068.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3068.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3068.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3068.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3068.PRE.filtered.gff jobid: 1355 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3068.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3068.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3068.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:03 2023] Finished job 1914. 1101 of 2231 steps (49%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:03 2023] Finished job 1355. 1102 of 2231 steps (49%) done [Fri Nov 3 10:37:07 2023] Finished job 422. 1103 of 2231 steps (49%) done [Fri Nov 3 10:37:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2691.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2691.PRE.gff, analyses/output/Amil-MirMachine/Mir-2691.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2691.PRE.unfiltered jobid: 421 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2691.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2691.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2691.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-963.PRE.CM output: analyses/output/Amil-MirMachine/Mir-963.PRE.result jobid: 1038 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-963.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-963.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:07 2023] Finished job 421. 1104 of 2231 steps (49%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2691.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2691.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2691.PRE.filtered.gff jobid: 1325 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2691.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2691.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2691.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2691.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2691.PRE.filtered.fasta jobid: 1884 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2691.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2691.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2691.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:07 2023] Finished job 1884. 1105 of 2231 steps (50%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:07 2023] Finished job 1325. 1106 of 2231 steps (50%) done [Fri Nov 3 10:37:08 2023] Finished job 1098. 1107 of 2231 steps (50%) done [Fri Nov 3 10:37:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9851.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9851.PRE.gff, analyses/output/Amil-MirMachine/Mir-9851.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9851.PRE.unfiltered jobid: 1097 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9851.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9851.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9851.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-358.PRE.CM output: analyses/output/Amil-MirMachine/Mir-358.PRE.result jobid: 558 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-358.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-358.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:08 2023] Finished job 1097. 1108 of 2231 steps (50%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9851.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9851.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9851.PRE.filtered.gff jobid: 1663 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9851.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9851.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9851.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9851.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9851.PRE.filtered.fasta jobid: 2222 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9851.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9851.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9851.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:08 2023] Finished job 2222. 1109 of 2231 steps (50%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:08 2023] Finished job 1663. 1110 of 2231 steps (50%) done [Fri Nov 3 10:37:16 2023] Finished job 1038. 1111 of 2231 steps (50%) done [Fri Nov 3 10:37:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-298.PRE.CM output: analyses/output/Amil-MirMachine/Mir-298.PRE.result jobid: 464 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-298.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-298.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-963.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-963.PRE.gff, analyses/output/Amil-MirMachine/Mir-963.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-963.PRE.unfiltered jobid: 1037 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-963.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-963.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-963.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] Finished job 1037. 1112 of 2231 steps (50%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-963.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-963.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-963.PRE.filtered.fasta jobid: 2192 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-963.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-963.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-963.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-963.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-963.PRE.filtered.gff jobid: 1633 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-963.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-963.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-963.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] Finished job 2192. 1113 of 2231 steps (50%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:17 2023] Finished job 1633. 1114 of 2231 steps (50%) done [Fri Nov 3 10:37:17 2023] Finished job 558. 1115 of 2231 steps (50%) done [Fri Nov 3 10:37:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3.PRE.result jobid: 468 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-358.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-358.PRE.gff, analyses/output/Amil-MirMachine/Mir-358.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-358.PRE.unfiltered jobid: 557 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-358.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-358.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-358.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] Finished job 557. 1116 of 2231 steps (50%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-358.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-358.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-358.PRE.filtered.fasta jobid: 1952 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-358.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-358.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-358.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-358.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-358.PRE.filtered.gff jobid: 1393 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-358.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-358.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-358.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:17 2023] Finished job 1952. 1117 of 2231 steps (50%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:18 2023] Finished job 1393. 1118 of 2231 steps (50%) done [Fri Nov 3 10:37:20 2023] Finished job 464. 1119 of 2231 steps (50%) done [Fri Nov 3 10:37:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4880.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4880.PRE.result jobid: 704 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4880.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4880.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-298.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-298.PRE.gff, analyses/output/Amil-MirMachine/Mir-298.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-298.PRE.unfiltered jobid: 463 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-298.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-298.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-298.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:20 2023] Finished job 463. 1120 of 2231 steps (50%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-298.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:21 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-298.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-298.PRE.filtered.gff jobid: 1346 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-298.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-298.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-298.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:21 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-298.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-298.PRE.filtered.fasta jobid: 1905 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-298.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-298.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-298.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:21 2023] Finished job 1905. 1121 of 2231 steps (50%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:21 2023] Finished job 1346. 1122 of 2231 steps (50%) done [Fri Nov 3 10:37:24 2023] Finished job 468. 1123 of 2231 steps (50%) done [Fri Nov 3 10:37:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3.PRE.gff, analyses/output/Amil-MirMachine/Mir-3.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3.PRE.unfiltered jobid: 467 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4888.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4888.PRE.result jobid: 710 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4888.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4888.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:24 2023] Finished job 467. 1124 of 2231 steps (50%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3.PRE.filtered.fasta jobid: 1907 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3.PRE.filtered.gff jobid: 1348 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:24 2023] Finished job 1907. 1125 of 2231 steps (50%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:25 2023] Finished job 1348. 1126 of 2231 steps (50%) done [Fri Nov 3 10:37:28 2023] Finished job 710. 1127 of 2231 steps (51%) done [Fri Nov 3 10:37:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-134.PRE.CM output: analyses/output/Amil-MirMachine/Mir-134.PRE.result jobid: 100 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-134.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-134.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4888.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4888.PRE.gff, analyses/output/Amil-MirMachine/Mir-4888.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4888.PRE.unfiltered jobid: 709 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4888.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4888.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4888.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] Finished job 704. 1128 of 2231 steps (51%) done Select jobs to execute... [Fri Nov 3 10:37:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-330.PRE.CM output: analyses/output/Amil-MirMachine/Mir-330.PRE.result jobid: 528 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-330.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-330.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4880.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4880.PRE.gff, analyses/output/Amil-MirMachine/Mir-4880.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4880.PRE.unfiltered jobid: 703 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4880.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4880.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4880.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] Finished job 709. 1129 of 2231 steps (51%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4888.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4888.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4888.PRE.filtered.fasta jobid: 2028 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4888.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4888.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4888.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4888.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4888.PRE.filtered.gff jobid: 1469 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4888.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4888.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4888.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] Finished job 703. 1130 of 2231 steps (51%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4880.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4880.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4880.PRE.filtered.gff jobid: 1466 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4880.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4880.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4880.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4880.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4880.PRE.filtered.fasta jobid: 2025 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4880.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4880.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4880.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:28 2023] Finished job 2028. 1131 of 2231 steps (51%) done Select jobs to execute... [Fri Nov 3 10:37:28 2023] Finished job 2025. 1132 of 2231 steps (51%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:37:28 2023] Finished job 1469. 1133 of 2231 steps (51%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:28 2023] Finished job 1466. 1134 of 2231 steps (51%) done [Fri Nov 3 10:37:32 2023] Finished job 100. 1135 of 2231 steps (51%) done [Fri Nov 3 10:37:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-134.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-134.PRE.gff, analyses/output/Amil-MirMachine/Mir-134.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-134.PRE.unfiltered jobid: 99 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-134.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-134.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-134.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-787.PRE.CM output: analyses/output/Amil-MirMachine/Mir-787.PRE.result jobid: 956 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-787.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-787.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:32 2023] Finished job 99. 1136 of 2231 steps (51%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-134.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-134.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-134.PRE.filtered.fasta jobid: 1723 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-134.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-134.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-134.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-134.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-134.PRE.filtered.gff jobid: 1164 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-134.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-134.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-134.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:32 2023] Finished job 1723. 1137 of 2231 steps (51%) done Select jobs to execute... [Fri Nov 3 10:37:32 2023] Finished job 528. 1138 of 2231 steps (51%) done [Fri Nov 3 10:37:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-330.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-330.PRE.gff, analyses/output/Amil-MirMachine/Mir-330.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-330.PRE.unfiltered jobid: 527 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-330.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-330.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-330.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9707.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9707.PRE.result jobid: 1070 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9707.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9707.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:32 2023] Finished job 527. 1139 of 2231 steps (51%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-330.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-330.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-330.PRE.filtered.gff jobid: 1378 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-330.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-330.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-330.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-330.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-330.PRE.filtered.fasta jobid: 1937 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-330.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-330.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-330.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:37:32 2023] Finished job 1937. 1140 of 2231 steps (51%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:32 2023] Finished job 1164. 1141 of 2231 steps (51%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:32 2023] Finished job 1378. 1142 of 2231 steps (51%) done [Fri Nov 3 10:37:37 2023] Finished job 1070. 1143 of 2231 steps (51%) done [Fri Nov 3 10:37:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-30.PRE.CM output: analyses/output/Amil-MirMachine/Mir-30.PRE.result jobid: 470 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-30.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-30.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9707.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9707.PRE.gff, analyses/output/Amil-MirMachine/Mir-9707.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9707.PRE.unfiltered jobid: 1069 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9707.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9707.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9707.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:37 2023] Finished job 1069. 1144 of 2231 steps (51%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9707.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9707.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9707.PRE.filtered.fasta jobid: 2208 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9707.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9707.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9707.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9707.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9707.PRE.filtered.gff jobid: 1649 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9707.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9707.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9707.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:37 2023] Finished job 2208. 1145 of 2231 steps (51%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:37 2023] Finished job 1649. 1146 of 2231 steps (51%) done [Fri Nov 3 10:37:43 2023] Finished job 956. 1147 of 2231 steps (51%) done [Fri Nov 3 10:37:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-964.PRE.CM output: analyses/output/Amil-MirMachine/Mir-964.PRE.result jobid: 1040 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-964.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-964.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-787.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-787.PRE.gff, analyses/output/Amil-MirMachine/Mir-787.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-787.PRE.unfiltered jobid: 955 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-787.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-787.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-787.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:43 2023] Finished job 955. 1148 of 2231 steps (51%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-787.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-787.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-787.PRE.filtered.fasta jobid: 2151 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-787.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-787.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-787.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-787.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-787.PRE.filtered.gff jobid: 1592 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-787.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-787.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-787.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:43 2023] Finished job 2151. 1149 of 2231 steps (52%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:44 2023] Finished job 1592. 1150 of 2231 steps (52%) done [Fri Nov 3 10:37:45 2023] Finished job 470. 1151 of 2231 steps (52%) done [Fri Nov 3 10:37:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-986.PRE.CM output: analyses/output/Amil-MirMachine/Mir-986.PRE.result jobid: 1100 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-986.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-986.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-30.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-30.PRE.gff, analyses/output/Amil-MirMachine/Mir-30.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-30.PRE.unfiltered jobid: 469 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-30.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-30.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-30.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:45 2023] Finished job 469. 1152 of 2231 steps (52%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-30.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-30.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-30.PRE.filtered.fasta jobid: 1908 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-30.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-30.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-30.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-30.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-30.PRE.filtered.gff jobid: 1349 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-30.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-30.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-30.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:45 2023] Finished job 1908. 1153 of 2231 steps (52%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:45 2023] Finished job 1349. 1154 of 2231 steps (52%) done [Fri Nov 3 10:37:50 2023] Finished job 1100. 1155 of 2231 steps (52%) done [Fri Nov 3 10:37:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-986.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-986.PRE.gff, analyses/output/Amil-MirMachine/Mir-986.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-986.PRE.unfiltered jobid: 1099 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-986.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-986.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-986.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1397.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1397.PRE.result jobid: 118 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1397.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1397.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:50 2023] Finished job 1099. 1156 of 2231 steps (52%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-986.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-986.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-986.PRE.filtered.fasta jobid: 2223 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-986.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-986.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-986.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-986.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-986.PRE.filtered.gff jobid: 1664 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-986.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-986.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-986.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:51 2023] Finished job 2223. 1157 of 2231 steps (52%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:51 2023] Finished job 1664. 1158 of 2231 steps (52%) done [Fri Nov 3 10:37:51 2023] Finished job 1040. 1159 of 2231 steps (52%) done [Fri Nov 3 10:37:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-964.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-964.PRE.gff, analyses/output/Amil-MirMachine/Mir-964.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-964.PRE.unfiltered jobid: 1039 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-964.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-964.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-964.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-944.PRE.CM output: analyses/output/Amil-MirMachine/Mir-944.PRE.result jobid: 1012 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-944.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-944.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:51 2023] Finished job 1039. 1160 of 2231 steps (52%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-964.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-964.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-964.PRE.filtered.fasta jobid: 2193 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-964.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-964.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-964.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-964.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-964.PRE.filtered.gff jobid: 1634 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-964.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-964.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-964.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:51 2023] Finished job 2193. 1161 of 2231 steps (52%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:52 2023] Finished job 1634. 1162 of 2231 steps (52%) done [Fri Nov 3 10:37:55 2023] Finished job 118. 1163 of 2231 steps (52%) done [Fri Nov 3 10:37:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-335.PRE.CM output: analyses/output/Amil-MirMachine/Mir-335.PRE.result jobid: 532 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-335.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-335.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:37:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1397.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1397.PRE.gff, analyses/output/Amil-MirMachine/Mir-1397.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1397.PRE.unfiltered jobid: 117 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1397.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1397.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1397.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:55 2023] Finished job 117. 1164 of 2231 steps (52%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1397.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:37:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1397.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1397.PRE.filtered.gff jobid: 1173 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1397.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1397.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1397.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1397.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1397.PRE.filtered.fasta jobid: 1732 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1397.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1397.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1397.PRE resources: tmpdir=/tmp [Fri Nov 3 10:37:55 2023] Finished job 1732. 1165 of 2231 steps (52%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:37:55 2023] Finished job 1173. 1166 of 2231 steps (52%) done [Fri Nov 3 10:38:03 2023] Finished job 1012. 1167 of 2231 steps (52%) done [Fri Nov 3 10:38:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-71.PRE.CM output: analyses/output/Amil-MirMachine/Mir-71.PRE.result jobid: 830 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-71.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-71.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-944.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-944.PRE.gff, analyses/output/Amil-MirMachine/Mir-944.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-944.PRE.unfiltered jobid: 1011 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-944.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-944.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-944.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:03 2023] Finished job 1011. 1168 of 2231 steps (52%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-944.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-944.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-944.PRE.filtered.fasta jobid: 2179 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-944.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-944.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-944.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-944.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-944.PRE.filtered.gff jobid: 1620 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-944.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-944.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-944.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:03 2023] Finished job 2179. 1169 of 2231 steps (52%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:03 2023] Finished job 1620. 1170 of 2231 steps (52%) done [Fri Nov 3 10:38:04 2023] Finished job 532. 1171 of 2231 steps (52%) done [Fri Nov 3 10:38:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4826.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4826.PRE.result jobid: 650 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4826.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4826.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-335.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-335.PRE.gff, analyses/output/Amil-MirMachine/Mir-335.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-335.PRE.unfiltered jobid: 531 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-335.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-335.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-335.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:04 2023] Finished job 531. 1172 of 2231 steps (53%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-335.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-335.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-335.PRE.filtered.fasta jobid: 1939 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-335.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-335.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-335.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-335.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-335.PRE.filtered.gff jobid: 1380 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-335.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-335.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-335.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:04 2023] Finished job 1939. 1173 of 2231 steps (53%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:04 2023] Finished job 1380. 1174 of 2231 steps (53%) done [Fri Nov 3 10:38:09 2023] Finished job 650. 1175 of 2231 steps (53%) done [Fri Nov 3 10:38:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-423.PRE.CM output: analyses/output/Amil-MirMachine/Mir-423.PRE.result jobid: 592 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-423.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-423.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4826.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4826.PRE.gff, analyses/output/Amil-MirMachine/Mir-4826.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4826.PRE.unfiltered jobid: 649 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4826.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4826.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4826.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] Finished job 649. 1176 of 2231 steps (53%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4826.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4826.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4826.PRE.filtered.gff jobid: 1439 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4826.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4826.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4826.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4826.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4826.PRE.filtered.fasta jobid: 1998 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4826.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4826.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4826.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] Finished job 1998. 1177 of 2231 steps (53%) done Select jobs to execute... [Fri Nov 3 10:38:09 2023] Finished job 830. 1178 of 2231 steps (53%) done [Fri Nov 3 10:38:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2019.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2019.PRE.result jobid: 292 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2019.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2019.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-71.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-71.PRE.gff, analyses/output/Amil-MirMachine/Mir-71.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-71.PRE.unfiltered jobid: 829 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-71.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-71.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-71.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] Finished job 829. 1179 of 2231 steps (53%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-71.PRE.ext.gff. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:38:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-71.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-71.PRE.filtered.fasta jobid: 2088 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-71.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-71.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-71.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-71.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-71.PRE.filtered.gff jobid: 1529 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-71.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-71.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-71.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:09 2023] Finished job 2088. 1180 of 2231 steps (53%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:09 2023] Finished job 1439. 1181 of 2231 steps (53%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:09 2023] Finished job 1529. 1182 of 2231 steps (53%) done [Fri Nov 3 10:38:12 2023] Finished job 592. 1183 of 2231 steps (53%) done [Fri Nov 3 10:38:12 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-303.PRE.CM output: analyses/output/Amil-MirMachine/Mir-303.PRE.result jobid: 472 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-303.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-303.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:12 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-423.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-423.PRE.gff, analyses/output/Amil-MirMachine/Mir-423.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-423.PRE.unfiltered jobid: 591 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-423.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-423.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-423.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:12 2023] Finished job 591. 1184 of 2231 steps (53%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-423.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-423.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-423.PRE.filtered.gff jobid: 1410 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-423.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-423.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-423.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-423.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-423.PRE.filtered.fasta jobid: 1969 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-423.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-423.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-423.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:13 2023] Finished job 1969. 1185 of 2231 steps (53%) done Select jobs to execute... [Fri Nov 3 10:38:13 2023] Finished job 292. 1186 of 2231 steps (53%) done [Fri Nov 3 10:38:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-489.PRE.CM output: analyses/output/Amil-MirMachine/Mir-489.PRE.result jobid: 712 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-489.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-489.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2019.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2019.PRE.gff, analyses/output/Amil-MirMachine/Mir-2019.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2019.PRE.unfiltered jobid: 291 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2019.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2019.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2019.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:38:13 2023] Finished job 291. 1187 of 2231 steps (53%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2019.PRE.ext.gff. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2019.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2019.PRE.filtered.fasta jobid: 1819 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2019.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2019.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2019.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2019.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2019.PRE.filtered.gff jobid: 1260 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2019.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2019.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2019.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:13 2023] Finished job 1410. 1188 of 2231 steps (53%) done Select jobs to execute... [Fri Nov 3 10:38:13 2023] Finished job 1819. 1189 of 2231 steps (53%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:13 2023] Finished job 1260. 1190 of 2231 steps (53%) done [Fri Nov 3 10:38:22 2023] Finished job 712. 1191 of 2231 steps (53%) done [Fri Nov 3 10:38:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7132.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7132.PRE.result jobid: 832 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7132.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7132.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-489.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-489.PRE.gff, analyses/output/Amil-MirMachine/Mir-489.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-489.PRE.unfiltered jobid: 711 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-489.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-489.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-489.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:23 2023] Finished job 711. 1192 of 2231 steps (53%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-489.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-489.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-489.PRE.filtered.gff jobid: 1470 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-489.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-489.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-489.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-489.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-489.PRE.filtered.fasta jobid: 2029 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-489.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-489.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-489.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:23 2023] Finished job 2029. 1193 of 2231 steps (53%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:23 2023] Finished job 1470. 1194 of 2231 steps (54%) done [Fri Nov 3 10:38:25 2023] Finished job 472. 1195 of 2231 steps (54%) done [Fri Nov 3 10:38:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4828.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4828.PRE.result jobid: 652 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4828.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4828.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-303.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-303.PRE.gff, analyses/output/Amil-MirMachine/Mir-303.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-303.PRE.unfiltered jobid: 471 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-303.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-303.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-303.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:25 2023] Finished job 471. 1196 of 2231 steps (54%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-303.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-303.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-303.PRE.filtered.gff jobid: 1350 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-303.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-303.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-303.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-303.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-303.PRE.filtered.fasta jobid: 1909 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-303.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-303.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-303.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:25 2023] Finished job 1909. 1197 of 2231 steps (54%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:26 2023] Finished job 1350. 1198 of 2231 steps (54%) done [Fri Nov 3 10:38:30 2023] Finished job 832. 1199 of 2231 steps (54%) done [Fri Nov 3 10:38:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-590.PRE.CM output: analyses/output/Amil-MirMachine/Mir-590.PRE.result jobid: 772 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-590.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-590.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7132.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7132.PRE.gff, analyses/output/Amil-MirMachine/Mir-7132.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7132.PRE.unfiltered jobid: 831 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7132.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7132.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7132.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:30 2023] Finished job 831. 1200 of 2231 steps (54%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7132.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7132.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7132.PRE.filtered.gff jobid: 1530 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7132.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7132.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7132.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7132.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7132.PRE.filtered.fasta jobid: 2089 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7132.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7132.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7132.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:30 2023] Finished job 2089. 1201 of 2231 steps (54%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:30 2023] Finished job 1530. 1202 of 2231 steps (54%) done [Fri Nov 3 10:38:40 2023] Finished job 772. 1203 of 2231 steps (54%) done [Fri Nov 3 10:38:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7323.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7323.PRE.result jobid: 892 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7323.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7323.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-590.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-590.PRE.gff, analyses/output/Amil-MirMachine/Mir-590.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-590.PRE.unfiltered jobid: 771 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-590.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-590.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-590.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:40 2023] Finished job 771. 1204 of 2231 steps (54%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-590.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-590.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-590.PRE.filtered.fasta jobid: 2059 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-590.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-590.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-590.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-590.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-590.PRE.filtered.gff jobid: 1500 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-590.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-590.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-590.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:40 2023] Finished job 2059. 1205 of 2231 steps (54%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:40 2023] Finished job 1500. 1206 of 2231 steps (54%) done [Fri Nov 3 10:38:41 2023] Finished job 652. 1207 of 2231 steps (54%) done [Fri Nov 3 10:38:41 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12358.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12358.PRE.result jobid: 52 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12358.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12358.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:41 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4828.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4828.PRE.gff, analyses/output/Amil-MirMachine/Mir-4828.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4828.PRE.unfiltered jobid: 651 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4828.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4828.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4828.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:41 2023] Finished job 651. 1208 of 2231 steps (54%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4828.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:41 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4828.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4828.PRE.filtered.fasta jobid: 1999 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4828.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4828.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4828.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:41 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4828.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4828.PRE.filtered.gff jobid: 1440 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4828.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4828.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4828.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:41 2023] Finished job 1999. 1209 of 2231 steps (54%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:41 2023] Finished job 1440. 1210 of 2231 steps (54%) done [Fri Nov 3 10:38:44 2023] Finished job 892. 1211 of 2231 steps (54%) done [Fri Nov 3 10:38:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-732.PRE.CM output: analyses/output/Amil-MirMachine/Mir-732.PRE.result jobid: 890 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-732.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-732.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7323.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7323.PRE.gff, analyses/output/Amil-MirMachine/Mir-7323.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7323.PRE.unfiltered jobid: 891 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7323.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7323.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7323.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:44 2023] Finished job 891. 1212 of 2231 steps (54%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7323.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7323.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7323.PRE.filtered.fasta jobid: 2119 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7323.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7323.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7323.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7323.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7323.PRE.filtered.gff jobid: 1560 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7323.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7323.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7323.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:44 2023] Finished job 2119. 1213 of 2231 steps (54%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:44 2023] Finished job 1560. 1214 of 2231 steps (54%) done [Fri Nov 3 10:38:49 2023] Finished job 52. 1215 of 2231 steps (54%) done [Fri Nov 3 10:38:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1641.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1641.PRE.result jobid: 172 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1641.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1641.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12358.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12358.PRE.gff, analyses/output/Amil-MirMachine/Mir-12358.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12358.PRE.unfiltered jobid: 51 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12358.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12358.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12358.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:49 2023] Finished job 51. 1216 of 2231 steps (55%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12358.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12358.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12358.PRE.filtered.fasta jobid: 1699 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12358.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12358.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12358.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12358.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12358.PRE.filtered.gff jobid: 1140 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12358.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12358.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12358.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:49 2023] Finished job 1699. 1217 of 2231 steps (55%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:50 2023] Finished job 1140. 1218 of 2231 steps (55%) done [Fri Nov 3 10:38:50 2023] Finished job 890. 1219 of 2231 steps (55%) done [Fri Nov 3 10:38:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2189.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2189.PRE.result jobid: 352 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2189.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2189.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-732.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-732.PRE.gff, analyses/output/Amil-MirMachine/Mir-732.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-732.PRE.unfiltered jobid: 889 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-732.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-732.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-732.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:50 2023] Finished job 889. 1220 of 2231 steps (55%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-732.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-732.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-732.PRE.filtered.gff jobid: 1559 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-732.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-732.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-732.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-732.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-732.PRE.filtered.fasta jobid: 2118 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-732.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-732.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-732.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:51 2023] Finished job 2118. 1221 of 2231 steps (55%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:51 2023] Finished job 1559. 1222 of 2231 steps (55%) done [Fri Nov 3 10:38:53 2023] Finished job 172. 1223 of 2231 steps (55%) done [Fri Nov 3 10:38:53 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3146.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3146.PRE.result jobid: 502 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3146.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3146.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:53 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1641.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1641.PRE.gff, analyses/output/Amil-MirMachine/Mir-1641.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1641.PRE.unfiltered jobid: 171 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1641.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1641.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1641.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:53 2023] Finished job 171. 1224 of 2231 steps (55%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1641.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1641.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1641.PRE.filtered.fasta jobid: 1759 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1641.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1641.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1641.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1641.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1641.PRE.filtered.gff jobid: 1200 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1641.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1641.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1641.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:53 2023] Finished job 1759. 1225 of 2231 steps (55%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:53 2023] Finished job 1200. 1226 of 2231 steps (55%) done [Fri Nov 3 10:38:55 2023] Finished job 352. 1227 of 2231 steps (55%) done [Fri Nov 3 10:38:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-138.PRE.CM output: analyses/output/Amil-MirMachine/Mir-138.PRE.result jobid: 112 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-138.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-138.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2189.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2189.PRE.gff, analyses/output/Amil-MirMachine/Mir-2189.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2189.PRE.unfiltered jobid: 351 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2189.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2189.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2189.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:56 2023] Finished job 351. 1228 of 2231 steps (55%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2189.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2189.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2189.PRE.filtered.gff jobid: 1290 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2189.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2189.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2189.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2189.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2189.PRE.filtered.fasta jobid: 1849 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2189.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2189.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2189.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:56 2023] Finished job 1849. 1229 of 2231 steps (55%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:56 2023] Finished job 1290. 1230 of 2231 steps (55%) done [Fri Nov 3 10:38:58 2023] Finished job 502. 1231 of 2231 steps (55%) done [Fri Nov 3 10:38:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3146.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3146.PRE.gff, analyses/output/Amil-MirMachine/Mir-3146.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3146.PRE.unfiltered jobid: 501 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3146.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-3146.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3146.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-361.PRE.CM output: analyses/output/Amil-MirMachine/Mir-361.PRE.result jobid: 562 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-361.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-361.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:38:58 2023] Finished job 501. 1232 of 2231 steps (55%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3146.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:38:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3146.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3146.PRE.filtered.gff jobid: 1365 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3146.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3146.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3146.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3146.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3146.PRE.filtered.fasta jobid: 1924 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3146.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3146.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3146.PRE resources: tmpdir=/tmp [Fri Nov 3 10:38:58 2023] Finished job 1924. 1233 of 2231 steps (55%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:38:59 2023] Finished job 1365. 1234 of 2231 steps (55%) done [Fri Nov 3 10:39:00 2023] Finished job 112. 1235 of 2231 steps (55%) done [Fri Nov 3 10:39:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2685.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2685.PRE.result jobid: 412 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2685.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2685.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-138.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-138.PRE.gff, analyses/output/Amil-MirMachine/Mir-138.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-138.PRE.unfiltered jobid: 111 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-138.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-138.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-138.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:01 2023] Finished job 111. 1236 of 2231 steps (55%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-138.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-138.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-138.PRE.filtered.gff jobid: 1170 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-138.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-138.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-138.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-138.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-138.PRE.filtered.fasta jobid: 1729 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-138.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-138.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-138.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:01 2023] Finished job 1729. 1237 of 2231 steps (55%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:01 2023] Finished job 1170. 1238 of 2231 steps (55%) done [Fri Nov 3 10:39:02 2023] Finished job 562. 1239 of 2231 steps (56%) done [Fri Nov 3 10:39:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-361.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-361.PRE.gff, analyses/output/Amil-MirMachine/Mir-361.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-361.PRE.unfiltered jobid: 561 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-361.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-361.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-361.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-278.PRE.CM output: analyses/output/Amil-MirMachine/Mir-278.PRE.result jobid: 442 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-278.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-278.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:02 2023] Finished job 561. 1240 of 2231 steps (56%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-361.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-361.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-361.PRE.filtered.fasta jobid: 1954 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-361.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-361.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-361.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-361.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-361.PRE.filtered.gff jobid: 1395 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-361.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-361.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-361.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:03 2023] Finished job 1954. 1241 of 2231 steps (56%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:03 2023] Finished job 1395. 1242 of 2231 steps (56%) done [Fri Nov 3 10:39:07 2023] Finished job 442. 1243 of 2231 steps (56%) done [Fri Nov 3 10:39:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-278.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-278.PRE.gff, analyses/output/Amil-MirMachine/Mir-278.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-278.PRE.unfiltered jobid: 441 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-278.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-278.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-278.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-615.PRE.CM output: analyses/output/Amil-MirMachine/Mir-615.PRE.result jobid: 782 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-615.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-615.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:07 2023] Finished job 441. 1244 of 2231 steps (56%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-278.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-278.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-278.PRE.filtered.fasta jobid: 1894 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-278.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-278.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-278.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-278.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-278.PRE.filtered.gff jobid: 1335 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-278.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-278.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-278.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:07 2023] Finished job 1894. 1245 of 2231 steps (56%) done Select jobs to execute... [Fri Nov 3 10:39:07 2023] Finished job 412. 1246 of 2231 steps (56%) done [Fri Nov 3 10:39:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-956.PRE.CM output: analyses/output/Amil-MirMachine/Mir-956.PRE.result jobid: 1022 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-956.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-956.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2685.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2685.PRE.gff, analyses/output/Amil-MirMachine/Mir-2685.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2685.PRE.unfiltered jobid: 411 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2685.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2685.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2685.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:07 2023] Finished job 411. 1247 of 2231 steps (56%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2685.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2685.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2685.PRE.filtered.fasta jobid: 1879 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2685.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2685.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2685.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:07 2023] Building DAG of jobs... rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2685.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2685.PRE.filtered.gff jobid: 1320 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2685.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2685.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2685.PRE resources: tmpdir=/tmp Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:39:08 2023] Finished job 1879. 1248 of 2231 steps (56%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:08 2023] Finished job 1335. 1249 of 2231 steps (56%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:08 2023] Finished job 1320. 1250 of 2231 steps (56%) done [Fri Nov 3 10:39:10 2023] Finished job 782. 1251 of 2231 steps (56%) done [Fri Nov 3 10:39:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-615.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-615.PRE.gff, analyses/output/Amil-MirMachine/Mir-615.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-615.PRE.unfiltered jobid: 781 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-615.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-615.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-615.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4835.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4835.PRE.result jobid: 662 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4835.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4835.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:11 2023] Finished job 781. 1252 of 2231 steps (56%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-615.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-615.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-615.PRE.filtered.gff jobid: 1505 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-615.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-615.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-615.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-615.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-615.PRE.filtered.fasta jobid: 2064 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-615.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-615.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-615.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:11 2023] Finished job 2064. 1253 of 2231 steps (56%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:11 2023] Finished job 1505. 1254 of 2231 steps (56%) done [Fri Nov 3 10:39:16 2023] Finished job 1022. 1255 of 2231 steps (56%) done [Fri Nov 3 10:39:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2007.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2007.PRE.result jobid: 272 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2007.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2007.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-956.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-956.PRE.gff, analyses/output/Amil-MirMachine/Mir-956.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-956.PRE.unfiltered jobid: 1021 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-956.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-956.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-956.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:16 2023] Finished job 1021. 1256 of 2231 steps (56%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-956.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-956.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-956.PRE.filtered.gff jobid: 1625 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-956.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-956.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-956.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-956.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-956.PRE.filtered.fasta jobid: 2184 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-956.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-956.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-956.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:16 2023] Finished job 2184. 1257 of 2231 steps (56%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:17 2023] Finished job 1625. 1258 of 2231 steps (56%) done [Fri Nov 3 10:39:17 2023] Finished job 662. 1259 of 2231 steps (56%) done [Fri Nov 3 10:39:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1180.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1180.PRE.result jobid: 36 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1180.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1180.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4835.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4835.PRE.gff, analyses/output/Amil-MirMachine/Mir-4835.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4835.PRE.unfiltered jobid: 661 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4835.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4835.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4835.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:17 2023] Finished job 661. 1260 of 2231 steps (56%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4835.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4835.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4835.PRE.filtered.gff jobid: 1445 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4835.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4835.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4835.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4835.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4835.PRE.filtered.fasta jobid: 2004 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4835.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4835.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4835.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:17 2023] Finished job 2004. 1261 of 2231 steps (57%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:17 2023] Finished job 1445. 1262 of 2231 steps (57%) done [Fri Nov 3 10:39:20 2023] Finished job 36. 1263 of 2231 steps (57%) done [Fri Nov 3 10:39:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2001.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2001.PRE.result jobid: 262 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2001.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2001.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1180.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1180.PRE.gff, analyses/output/Amil-MirMachine/Mir-1180.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1180.PRE.unfiltered jobid: 35 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1180.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1180.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1180.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:20 2023] Finished job 35. 1264 of 2231 steps (57%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1180.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1180.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1180.PRE.filtered.fasta jobid: 1691 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1180.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1180.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1180.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1180.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1180.PRE.filtered.gff jobid: 1132 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1180.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1180.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1180.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:20 2023] Finished job 1691. 1265 of 2231 steps (57%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:21 2023] Finished job 1132. 1266 of 2231 steps (57%) done [Fri Nov 3 10:39:23 2023] Finished job 272. 1267 of 2231 steps (57%) done [Fri Nov 3 10:39:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2114.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2114.PRE.result jobid: 336 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2114.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2114.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2007.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2007.PRE.gff, analyses/output/Amil-MirMachine/Mir-2007.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2007.PRE.unfiltered jobid: 271 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2007.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2007.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2007.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:23 2023] Finished job 271. 1268 of 2231 steps (57%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2007.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2007.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2007.PRE.filtered.gff jobid: 1250 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2007.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2007.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2007.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2007.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2007.PRE.filtered.fasta jobid: 1809 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2007.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2007.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2007.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:23 2023] Finished job 1809. 1269 of 2231 steps (57%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:23 2023] Finished job 1250. 1270 of 2231 steps (57%) done [Fri Nov 3 10:39:27 2023] Finished job 262. 1271 of 2231 steps (57%) done [Fri Nov 3 10:39:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2001.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2001.PRE.gff, analyses/output/Amil-MirMachine/Mir-2001.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2001.PRE.unfiltered jobid: 261 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2001.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2001.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2001.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-216.PRE.CM output: analyses/output/Amil-MirMachine/Mir-216.PRE.result jobid: 342 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-216.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-216.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:27 2023] Finished job 261. 1272 of 2231 steps (57%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2001.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2001.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2001.PRE.filtered.gff jobid: 1245 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2001.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2001.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2001.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2001.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2001.PRE.filtered.fasta jobid: 1804 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2001.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2001.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2001.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:27 2023] Finished job 1804. 1273 of 2231 steps (57%) done Select jobs to execute... [Fri Nov 3 10:39:28 2023] Finished job 336. 1274 of 2231 steps (57%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:39:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4864.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4864.PRE.result jobid: 682 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4864.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4864.PRE threads: 15 resources: tmpdir=/tmp ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2114.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2114.PRE.gff, analyses/output/Amil-MirMachine/Mir-2114.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2114.PRE.unfiltered jobid: 335 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2114.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2114.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2114.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:28 2023] Finished job 1245. 1275 of 2231 steps (57%) done Select jobs to execute... [Fri Nov 3 10:39:28 2023] Finished job 335. 1276 of 2231 steps (57%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2114.PRE.ext.gff. [Fri Nov 3 10:39:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2114.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2114.PRE.filtered.fasta jobid: 1841 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2114.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2114.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2114.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2114.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2114.PRE.filtered.gff jobid: 1282 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2114.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2114.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2114.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:28 2023] Finished job 1841. 1277 of 2231 steps (57%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:28 2023] Finished job 1282. 1278 of 2231 steps (57%) done [Fri Nov 3 10:39:31 2023] Finished job 682. 1279 of 2231 steps (57%) done [Fri Nov 3 10:39:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4864.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4864.PRE.gff, analyses/output/Amil-MirMachine/Mir-4864.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4864.PRE.unfiltered jobid: 681 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4864.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4864.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4864.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12086.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12086.PRE.result jobid: 42 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12086.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12086.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:31 2023] Finished job 681. 1280 of 2231 steps (57%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4864.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4864.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4864.PRE.filtered.fasta jobid: 2014 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4864.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4864.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4864.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4864.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4864.PRE.filtered.gff jobid: 1455 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4864.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4864.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4864.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:31 2023] Finished job 2014. 1281 of 2231 steps (57%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:32 2023] Finished job 1455. 1282 of 2231 steps (57%) done [Fri Nov 3 10:39:32 2023] Finished job 342. 1283 of 2231 steps (58%) done [Fri Nov 3 10:39:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-666.PRE.CM output: analyses/output/Amil-MirMachine/Mir-666.PRE.result jobid: 802 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-666.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-666.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-216.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-216.PRE.gff, analyses/output/Amil-MirMachine/Mir-216.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-216.PRE.unfiltered jobid: 341 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-216.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-216.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-216.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:32 2023] Finished job 341. 1284 of 2231 steps (58%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-216.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-216.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-216.PRE.filtered.gff jobid: 1285 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-216.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-216.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-216.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-216.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-216.PRE.filtered.fasta jobid: 1844 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-216.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-216.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-216.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:32 2023] Finished job 1844. 1285 of 2231 steps (58%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:32 2023] Finished job 1285. 1286 of 2231 steps (58%) done [Fri Nov 3 10:39:34 2023] Finished job 42. 1287 of 2231 steps (58%) done [Fri Nov 3 10:39:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12366.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12366.PRE.result jobid: 54 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12366.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12366.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12086.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12086.PRE.gff, analyses/output/Amil-MirMachine/Mir-12086.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12086.PRE.unfiltered jobid: 41 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12086.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12086.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12086.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:34 2023] Finished job 41. 1288 of 2231 steps (58%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12086.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12086.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12086.PRE.filtered.fasta jobid: 1694 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12086.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12086.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12086.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12086.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12086.PRE.filtered.gff jobid: 1135 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12086.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12086.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12086.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:35 2023] Finished job 1694. 1289 of 2231 steps (58%) done Select jobs to execute... [Fri Nov 3 10:39:35 2023] Finished job 802. 1290 of 2231 steps (58%) done [Fri Nov 3 10:39:35 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-666.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-666.PRE.gff, analyses/output/Amil-MirMachine/Mir-666.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-666.PRE.unfiltered jobid: 801 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-666.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-666.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-666.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:35 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-219.PRE.CM output: analyses/output/Amil-MirMachine/Mir-219.PRE.result jobid: 354 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-219.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-219.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:35 2023] Finished job 801. 1291 of 2231 steps (58%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-666.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-666.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-666.PRE.filtered.fasta jobid: 2074 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-666.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-666.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-666.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-666.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-666.PRE.filtered.gff jobid: 1515 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-666.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-666.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-666.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:39:35 2023] Finished job 2074. 1292 of 2231 steps (58%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:35 2023] Finished job 1135. 1293 of 2231 steps (58%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:35 2023] Finished job 1515. 1294 of 2231 steps (58%) done [Fri Nov 3 10:39:38 2023] Finished job 54. 1295 of 2231 steps (58%) done [Fri Nov 3 10:39:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-971.PRE.CM output: analyses/output/Amil-MirMachine/Mir-971.PRE.result jobid: 1072 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-971.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-971.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12366.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12366.PRE.gff, analyses/output/Amil-MirMachine/Mir-12366.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12366.PRE.unfiltered jobid: 53 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12366.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12366.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12366.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:38 2023] Finished job 53. 1296 of 2231 steps (58%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12366.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12366.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12366.PRE.filtered.gff jobid: 1141 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12366.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12366.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12366.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12366.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12366.PRE.filtered.fasta jobid: 1700 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12366.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12366.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12366.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:38 2023] Finished job 1700. 1297 of 2231 steps (58%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:38 2023] Finished job 1141. 1298 of 2231 steps (58%) done [Fri Nov 3 10:39:40 2023] Finished job 354. 1299 of 2231 steps (58%) done [Fri Nov 3 10:39:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1985.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1985.PRE.result jobid: 232 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1985.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1985.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-219.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-219.PRE.gff, analyses/output/Amil-MirMachine/Mir-219.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-219.PRE.unfiltered jobid: 353 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-219.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-219.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-219.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:40 2023] Finished job 353. 1300 of 2231 steps (58%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-219.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-219.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-219.PRE.filtered.fasta jobid: 1850 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-219.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-219.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-219.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-219.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-219.PRE.filtered.gff jobid: 1291 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-219.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-219.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-219.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:40 2023] Finished job 1850. 1301 of 2231 steps (58%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:41 2023] Finished job 1291. 1302 of 2231 steps (58%) done [Fri Nov 3 10:39:46 2023] Finished job 1072. 1303 of 2231 steps (58%) done [Fri Nov 3 10:39:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-971.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-971.PRE.gff, analyses/output/Amil-MirMachine/Mir-971.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-971.PRE.unfiltered jobid: 1071 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-971.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-971.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-971.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-987.PRE.CM output: analyses/output/Amil-MirMachine/Mir-987.PRE.result jobid: 1102 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-987.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-987.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:46 2023] Finished job 1071. 1304 of 2231 steps (58%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-971.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-971.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-971.PRE.filtered.gff jobid: 1650 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-971.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-971.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-971.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-971.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-971.PRE.filtered.fasta jobid: 2209 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-971.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-971.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-971.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:46 2023] Finished job 2209. 1305 of 2231 steps (58%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:46 2023] Finished job 1650. 1306 of 2231 steps (59%) done [Fri Nov 3 10:39:50 2023] Finished job 232. 1307 of 2231 steps (59%) done [Fri Nov 3 10:39:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12355.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12355.PRE.result jobid: 50 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12355.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12355.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1985.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1985.PRE.gff, analyses/output/Amil-MirMachine/Mir-1985.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1985.PRE.unfiltered jobid: 231 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1985.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1985.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1985.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:50 2023] Finished job 231. 1308 of 2231 steps (59%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1985.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1985.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1985.PRE.filtered.gff jobid: 1230 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1985.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1985.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1985.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1985.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1985.PRE.filtered.fasta jobid: 1789 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1985.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1985.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1985.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:50 2023] Finished job 1789. 1309 of 2231 steps (59%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:50 2023] Finished job 1230. 1310 of 2231 steps (59%) done [Fri Nov 3 10:39:52 2023] Finished job 1102. 1311 of 2231 steps (59%) done [Fri Nov 3 10:39:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-987.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-987.PRE.gff, analyses/output/Amil-MirMachine/Mir-987.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-987.PRE.unfiltered jobid: 1101 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-987.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-987.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-987.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-965.PRE.CM output: analyses/output/Amil-MirMachine/Mir-965.PRE.result jobid: 1042 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-965.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-965.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:52 2023] Finished job 1101. 1312 of 2231 steps (59%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-987.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-987.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-987.PRE.filtered.fasta jobid: 2224 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-987.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-987.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-987.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-987.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-987.PRE.filtered.gff jobid: 1665 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-987.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-987.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-987.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:52 2023] Finished job 2224. 1313 of 2231 steps (59%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:52 2023] Finished job 1665. 1314 of 2231 steps (59%) done [Fri Nov 3 10:39:53 2023] Finished job 50. 1315 of 2231 steps (59%) done [Fri Nov 3 10:39:53 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4818.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4818.PRE.result jobid: 640 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4818.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4818.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:53 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12355.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12355.PRE.gff, analyses/output/Amil-MirMachine/Mir-12355.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12355.PRE.unfiltered jobid: 49 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12355.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12355.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:53 2023] Finished job 49. 1316 of 2231 steps (59%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12355.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12355.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12355.PRE.filtered.gff jobid: 1139 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12355.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12355.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12355.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12355.PRE.filtered.fasta jobid: 1698 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12355.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12355.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:53 2023] Finished job 1698. 1317 of 2231 steps (59%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:54 2023] Finished job 1139. 1318 of 2231 steps (59%) done [Fri Nov 3 10:39:59 2023] Finished job 1042. 1319 of 2231 steps (59%) done [Fri Nov 3 10:39:59 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-965.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-965.PRE.gff, analyses/output/Amil-MirMachine/Mir-965.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-965.PRE.unfiltered jobid: 1041 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-965.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-965.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-965.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:59 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-73.PRE.CM output: analyses/output/Amil-MirMachine/Mir-73.PRE.result jobid: 880 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-73.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-73.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:39:59 2023] Finished job 1041. 1320 of 2231 steps (59%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-965.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:39:59 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-965.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-965.PRE.filtered.fasta jobid: 2194 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-965.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-965.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-965.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:59 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-965.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-965.PRE.filtered.gff jobid: 1635 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-965.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-965.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-965.PRE resources: tmpdir=/tmp [Fri Nov 3 10:39:59 2023] Finished job 2194. 1321 of 2231 steps (59%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:39:59 2023] Finished job 1635. 1322 of 2231 steps (59%) done [Fri Nov 3 10:40:02 2023] Finished job 640. 1323 of 2231 steps (59%) done [Fri Nov 3 10:40:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4818.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4818.PRE.gff, analyses/output/Amil-MirMachine/Mir-4818.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4818.PRE.unfiltered jobid: 639 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4818.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4818.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4818.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1559.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1559.PRE.result jobid: 170 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1559.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1559.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:02 2023] Finished job 639. 1324 of 2231 steps (59%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4818.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4818.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4818.PRE.filtered.fasta jobid: 1993 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4818.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4818.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4818.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4818.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4818.PRE.filtered.gff jobid: 1434 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4818.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4818.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4818.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:02 2023] Finished job 1993. 1325 of 2231 steps (59%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:03 2023] Finished job 1434. 1326 of 2231 steps (59%) done [Fri Nov 3 10:40:04 2023] Finished job 880. 1327 of 2231 steps (59%) done [Fri Nov 3 10:40:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-73.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-73.PRE.gff, analyses/output/Amil-MirMachine/Mir-73.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-73.PRE.unfiltered jobid: 879 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-73.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-73.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-73.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1984.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1984.PRE.result jobid: 230 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1984.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1984.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:04 2023] Finished job 879. 1328 of 2231 steps (60%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-73.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-73.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-73.PRE.filtered.fasta jobid: 2113 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-73.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-73.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-73.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-73.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-73.PRE.filtered.gff jobid: 1554 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-73.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-73.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-73.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:04 2023] Finished job 2113. 1329 of 2231 steps (60%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:05 2023] Finished job 1554. 1330 of 2231 steps (60%) done [Fri Nov 3 10:40:06 2023] Finished job 170. 1331 of 2231 steps (60%) done [Fri Nov 3 10:40:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4824.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4824.PRE.result jobid: 646 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4824.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4824.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1559.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1559.PRE.gff, analyses/output/Amil-MirMachine/Mir-1559.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1559.PRE.unfiltered jobid: 169 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1559.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1559.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1559.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:06 2023] Finished job 169. 1332 of 2231 steps (60%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1559.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1559.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1559.PRE.filtered.gff jobid: 1199 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1559.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1559.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1559.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1559.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1559.PRE.filtered.fasta jobid: 1758 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1559.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1559.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1559.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:06 2023] Finished job 1758. 1333 of 2231 steps (60%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:07 2023] Finished job 1199. 1334 of 2231 steps (60%) done [Fri Nov 3 10:40:09 2023] Finished job 230. 1335 of 2231 steps (60%) done [Fri Nov 3 10:40:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7309.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7309.PRE.result jobid: 886 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7309.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7309.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1984.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1984.PRE.gff, analyses/output/Amil-MirMachine/Mir-1984.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1984.PRE.unfiltered jobid: 229 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1984.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1984.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:09 2023] Finished job 229. 1336 of 2231 steps (60%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1984.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1984.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1984.PRE.filtered.fasta jobid: 1788 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1984.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1984.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1984.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1984.PRE.filtered.gff jobid: 1229 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1984.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1984.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:09 2023] Finished job 1788. 1337 of 2231 steps (60%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:09 2023] Finished job 1229. 1338 of 2231 steps (60%) done [Fri Nov 3 10:40:13 2023] Finished job 886. 1339 of 2231 steps (60%) done [Fri Nov 3 10:40:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7309.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7309.PRE.gff, analyses/output/Amil-MirMachine/Mir-7309.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7309.PRE.unfiltered jobid: 885 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7309.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7309.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7309.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2188.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2188.PRE.result jobid: 350 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2188.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2188.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:13 2023] Finished job 885. 1340 of 2231 steps (60%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7309.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7309.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7309.PRE.filtered.fasta jobid: 2116 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7309.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7309.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7309.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7309.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7309.PRE.filtered.gff jobid: 1557 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7309.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7309.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7309.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:13 2023] Finished job 2116. 1341 of 2231 steps (60%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:13 2023] Finished job 1557. 1342 of 2231 steps (60%) done [Fri Nov 3 10:40:18 2023] Finished job 646. 1343 of 2231 steps (60%) done [Fri Nov 3 10:40:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4824.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4824.PRE.gff, analyses/output/Amil-MirMachine/Mir-4824.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4824.PRE.unfiltered jobid: 645 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4824.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4824.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4824.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-95.PRE.CM output: analyses/output/Amil-MirMachine/Mir-95.PRE.result jobid: 1014 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-95.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-95.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:18 2023] Finished job 645. 1344 of 2231 steps (60%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4824.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:18 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4824.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4824.PRE.filtered.fasta jobid: 1996 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4824.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4824.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4824.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:18 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4824.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4824.PRE.filtered.gff jobid: 1437 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4824.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4824.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4824.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:18 2023] Finished job 1996. 1345 of 2231 steps (60%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:18 2023] Finished job 1437. 1346 of 2231 steps (60%) done [Fri Nov 3 10:40:18 2023] Finished job 350. 1347 of 2231 steps (60%) done [Fri Nov 3 10:40:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4829.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4829.PRE.result jobid: 654 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4829.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4829.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2188.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2188.PRE.gff, analyses/output/Amil-MirMachine/Mir-2188.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2188.PRE.unfiltered jobid: 349 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2188.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2188.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2188.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:18 2023] Finished job 349. 1348 of 2231 steps (60%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2188.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:19 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2188.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2188.PRE.filtered.fasta jobid: 1848 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2188.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2188.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2188.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:19 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2188.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2188.PRE.filtered.gff jobid: 1289 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2188.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2188.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2188.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:19 2023] Finished job 1848. 1349 of 2231 steps (60%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:19 2023] Finished job 1289. 1350 of 2231 steps (61%) done [Fri Nov 3 10:40:31 2023] Finished job 1014. 1351 of 2231 steps (61%) done [Fri Nov 3 10:40:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-95.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-95.PRE.gff, analyses/output/Amil-MirMachine/Mir-95.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-95.PRE.unfiltered jobid: 1013 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-95.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-95.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-95.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2002.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2002.PRE.result jobid: 264 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2002.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2002.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:31 2023] Finished job 1013. 1352 of 2231 steps (61%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-95.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-95.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-95.PRE.filtered.fasta jobid: 2180 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-95.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-95.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-95.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-95.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-95.PRE.filtered.gff jobid: 1621 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-95.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-95.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-95.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:31 2023] Finished job 2180. 1353 of 2231 steps (61%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:31 2023] Finished job 1621. 1354 of 2231 steps (61%) done [Fri Nov 3 10:40:32 2023] Finished job 654. 1355 of 2231 steps (61%) done [Fri Nov 3 10:40:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4829.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4829.PRE.gff, analyses/output/Amil-MirMachine/Mir-4829.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4829.PRE.unfiltered jobid: 653 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4829.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4829.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4829.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-315.PRE.CM output: analyses/output/Amil-MirMachine/Mir-315.PRE.result jobid: 504 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-315.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-315.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:32 2023] Finished job 653. 1356 of 2231 steps (61%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4829.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4829.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4829.PRE.filtered.fasta jobid: 2000 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4829.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4829.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4829.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4829.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4829.PRE.filtered.gff jobid: 1441 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4829.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4829.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4829.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:32 2023] Finished job 2000. 1357 of 2231 steps (61%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:33 2023] Finished job 1441. 1358 of 2231 steps (61%) done [Fri Nov 3 10:40:38 2023] Finished job 264. 1359 of 2231 steps (61%) done [Fri Nov 3 10:40:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2002.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2002.PRE.gff, analyses/output/Amil-MirMachine/Mir-2002.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2002.PRE.unfiltered jobid: 263 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2002.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2002.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2002.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-279.PRE.CM output: analyses/output/Amil-MirMachine/Mir-279.PRE.result jobid: 444 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-279.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-279.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:38 2023] Finished job 263. 1360 of 2231 steps (61%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2002.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2002.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2002.PRE.filtered.fasta jobid: 1805 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2002.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2002.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2002.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2002.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2002.PRE.filtered.gff jobid: 1246 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2002.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2002.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2002.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:38 2023] Finished job 1805. 1361 of 2231 steps (61%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:39 2023] Finished job 1246. 1362 of 2231 steps (61%) done [Fri Nov 3 10:40:40 2023] Finished job 504. 1363 of 2231 steps (61%) done [Fri Nov 3 10:40:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-315.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-315.PRE.gff, analyses/output/Amil-MirMachine/Mir-315.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-315.PRE.unfiltered jobid: 503 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-315.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-315.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-315.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-282.PRE.CM output: analyses/output/Amil-MirMachine/Mir-282.PRE.result jobid: 452 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-282.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-282.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:40 2023] Finished job 503. 1364 of 2231 steps (61%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-315.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:41 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-315.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-315.PRE.filtered.fasta jobid: 1925 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-315.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-315.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-315.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:41 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-315.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-315.PRE.filtered.gff jobid: 1366 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-315.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-315.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-315.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:41 2023] Finished job 1925. 1365 of 2231 steps (61%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:41 2023] Finished job 1366. 1366 of 2231 steps (61%) done [Fri Nov 3 10:40:43 2023] Finished job 444. 1367 of 2231 steps (61%) done [Fri Nov 3 10:40:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-279.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-279.PRE.gff, analyses/output/Amil-MirMachine/Mir-279.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-279.PRE.unfiltered jobid: 443 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-279.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-279.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-279.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4872.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4872.PRE.result jobid: 692 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4872.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4872.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:43 2023] Finished job 443. 1368 of 2231 steps (61%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-279.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-279.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-279.PRE.filtered.gff jobid: 1336 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-279.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-279.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-279.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-279.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-279.PRE.filtered.fasta jobid: 1895 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-279.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-279.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-279.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:43 2023] Finished job 1895. 1369 of 2231 steps (61%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:43 2023] Finished job 1336. 1370 of 2231 steps (61%) done [Fri Nov 3 10:40:46 2023] Finished job 452. 1371 of 2231 steps (61%) done [Fri Nov 3 10:40:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-282.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-282.PRE.gff, analyses/output/Amil-MirMachine/Mir-282.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-282.PRE.unfiltered jobid: 451 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-282.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-282.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-282.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-667.PRE.CM output: analyses/output/Amil-MirMachine/Mir-667.PRE.result jobid: 804 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-667.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-667.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:47 2023] Finished job 451. 1372 of 2231 steps (61%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-282.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:47 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-282.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-282.PRE.filtered.fasta jobid: 1899 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-282.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-282.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-282.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:47 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-282.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-282.PRE.filtered.gff jobid: 1340 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-282.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-282.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-282.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:47 2023] Finished job 1899. 1373 of 2231 steps (62%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:47 2023] Finished job 1340. 1374 of 2231 steps (62%) done [Fri Nov 3 10:40:51 2023] Finished job 804. 1375 of 2231 steps (62%) done [Fri Nov 3 10:40:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-667.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-667.PRE.gff, analyses/output/Amil-MirMachine/Mir-667.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-667.PRE.unfiltered jobid: 803 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-667.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-667.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-667.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-676.PRE.CM output: analyses/output/Amil-MirMachine/Mir-676.PRE.result jobid: 822 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-676.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-676.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] Finished job 692. 1376 of 2231 steps (62%) done Select jobs to execute... [Fri Nov 3 10:40:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1662.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1662.PRE.result jobid: 174 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1662.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1662.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4872.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4872.PRE.gff, analyses/output/Amil-MirMachine/Mir-4872.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4872.PRE.unfiltered jobid: 691 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4872.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4872.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4872.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] Finished job 803. 1377 of 2231 steps (62%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-667.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-667.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-667.PRE.filtered.gff jobid: 1516 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-667.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-667.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-667.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-667.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-667.PRE.filtered.fasta jobid: 2075 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-667.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-667.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-667.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] Finished job 691. 1378 of 2231 steps (62%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4872.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4872.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4872.PRE.filtered.fasta jobid: 2019 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4872.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4872.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4872.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4872.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4872.PRE.filtered.gff jobid: 1460 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4872.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4872.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4872.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:51 2023] Finished job 2075. 1379 of 2231 steps (62%) done Select jobs to execute... [Fri Nov 3 10:40:51 2023] Finished job 2019. 1380 of 2231 steps (62%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:40:52 2023] Finished job 1516. 1381 of 2231 steps (62%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:52 2023] Finished job 1460. 1382 of 2231 steps (62%) done [Fri Nov 3 10:40:56 2023] Finished job 822. 1383 of 2231 steps (62%) done [Fri Nov 3 10:40:57 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4865.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4865.PRE.result jobid: 684 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4865.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4865.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:57 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-676.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-676.PRE.gff, analyses/output/Amil-MirMachine/Mir-676.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-676.PRE.unfiltered jobid: 821 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-676.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-676.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-676.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:57 2023] Finished job 821. 1384 of 2231 steps (62%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-676.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:57 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-676.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-676.PRE.filtered.gff jobid: 1525 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-676.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-676.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-676.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:57 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-676.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-676.PRE.filtered.fasta jobid: 2084 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-676.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-676.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-676.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:57 2023] Finished job 2084. 1385 of 2231 steps (62%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:57 2023] Finished job 1525. 1386 of 2231 steps (62%) done [Fri Nov 3 10:40:57 2023] Finished job 174. 1387 of 2231 steps (62%) done [Fri Nov 3 10:40:57 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1662.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1662.PRE.gff, analyses/output/Amil-MirMachine/Mir-1662.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1662.PRE.unfiltered jobid: 173 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1662.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1662.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1662.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:57 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1986.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1986.PRE.result jobid: 234 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1986.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1986.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:40:58 2023] Finished job 173. 1388 of 2231 steps (62%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1662.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:40:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1662.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1662.PRE.filtered.fasta jobid: 1760 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1662.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1662.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1662.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1662.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1662.PRE.filtered.gff jobid: 1201 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1662.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1662.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1662.PRE resources: tmpdir=/tmp [Fri Nov 3 10:40:58 2023] Finished job 1760. 1389 of 2231 steps (62%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:40:58 2023] Finished job 1201. 1390 of 2231 steps (62%) done [Fri Nov 3 10:41:00 2023] Finished job 684. 1391 of 2231 steps (62%) done [Fri Nov 3 10:41:00 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-785.PRE.CM output: analyses/output/Amil-MirMachine/Mir-785.PRE.result jobid: 954 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-785.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-785.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:00 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4865.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4865.PRE.gff, analyses/output/Amil-MirMachine/Mir-4865.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4865.PRE.unfiltered jobid: 683 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4865.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4865.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4865.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:00 2023] Finished job 683. 1392 of 2231 steps (62%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4865.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:00 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4865.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4865.PRE.filtered.gff jobid: 1456 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4865.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4865.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4865.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:00 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4865.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4865.PRE.filtered.fasta jobid: 2015 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4865.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4865.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4865.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:00 2023] Finished job 2015. 1393 of 2231 steps (62%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:00 2023] Finished job 1456. 1394 of 2231 steps (62%) done [Fri Nov 3 10:41:02 2023] Finished job 234. 1395 of 2231 steps (63%) done [Fri Nov 3 10:41:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1986.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1986.PRE.gff, analyses/output/Amil-MirMachine/Mir-1986.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1986.PRE.unfiltered jobid: 233 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1986.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1986.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1986.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3613.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3613.PRE.result jobid: 564 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3613.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3613.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:02 2023] Finished job 233. 1396 of 2231 steps (63%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1986.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1986.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1986.PRE.filtered.gff jobid: 1231 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1986.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1986.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1986.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1986.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1986.PRE.filtered.fasta jobid: 1790 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1986.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1986.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1986.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:02 2023] Finished job 1790. 1397 of 2231 steps (63%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:03 2023] Finished job 1231. 1398 of 2231 steps (63%) done [Fri Nov 3 10:41:08 2023] Finished job 954. 1399 of 2231 steps (63%) done [Fri Nov 3 10:41:08 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-785.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-785.PRE.gff, analyses/output/Amil-MirMachine/Mir-785.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-785.PRE.unfiltered jobid: 953 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-785.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-785.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-785.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:08 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1388.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1388.PRE.result jobid: 114 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1388.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1388.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:08 2023] Finished job 953. 1400 of 2231 steps (63%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-785.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:08 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-785.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-785.PRE.filtered.fasta jobid: 2150 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-785.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-785.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-785.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:08 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-785.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-785.PRE.filtered.gff jobid: 1591 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-785.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-785.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-785.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:08 2023] Finished job 2150. 1401 of 2231 steps (63%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:08 2023] Finished job 1591. 1402 of 2231 steps (63%) done [Fri Nov 3 10:41:14 2023] Finished job 114. 1403 of 2231 steps (63%) done [Fri Nov 3 10:41:14 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1388.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1388.PRE.gff, analyses/output/Amil-MirMachine/Mir-1388.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1388.PRE.unfiltered jobid: 113 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1388.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1388.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1388.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:14 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7327.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7327.PRE.result jobid: 894 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7327.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7327.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:14 2023] Finished job 113. 1404 of 2231 steps (63%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1388.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1388.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1388.PRE.filtered.fasta jobid: 1730 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1388.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1388.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1388.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1388.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1388.PRE.filtered.gff jobid: 1171 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1388.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1388.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1388.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:14 2023] Finished job 1730. 1405 of 2231 steps (63%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:14 2023] Finished job 1171. 1406 of 2231 steps (63%) done [Fri Nov 3 10:41:17 2023] Finished job 894. 1407 of 2231 steps (63%) done [Fri Nov 3 10:41:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-934.PRE.CM output: analyses/output/Amil-MirMachine/Mir-934.PRE.result jobid: 1004 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-934.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-934.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7327.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7327.PRE.gff, analyses/output/Amil-MirMachine/Mir-7327.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7327.PRE.unfiltered jobid: 893 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7327.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7327.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7327.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:17 2023] Finished job 893. 1408 of 2231 steps (63%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7327.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7327.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7327.PRE.filtered.fasta jobid: 2120 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7327.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7327.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7327.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7327.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7327.PRE.filtered.gff jobid: 1561 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7327.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7327.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7327.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:18 2023] Finished job 2120. 1409 of 2231 steps (63%) done Select jobs to execute... [Fri Nov 3 10:41:18 2023] Finished job 564. 1410 of 2231 steps (63%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:41:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3613.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3613.PRE.gff, analyses/output/Amil-MirMachine/Mir-3613.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3613.PRE.unfiltered jobid: 563 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3613.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3613.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3613.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9388.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9388.PRE.result jobid: 1010 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9388.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9388.PRE threads: 15 resources: tmpdir=/tmp ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:18 2023] Finished job 563. 1411 of 2231 steps (63%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3613.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:18 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3613.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3613.PRE.filtered.gff jobid: 1396 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3613.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3613.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3613.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:18 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3613.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3613.PRE.filtered.fasta jobid: 1955 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3613.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3613.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3613.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:18 2023] Finished job 1561. 1412 of 2231 steps (63%) done Select jobs to execute... [Fri Nov 3 10:41:18 2023] Finished job 1955. 1413 of 2231 steps (63%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:18 2023] Finished job 1396. 1414 of 2231 steps (63%) done [Fri Nov 3 10:41:21 2023] Finished job 1004. 1415 of 2231 steps (63%) done [Fri Nov 3 10:41:21 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-988.PRE.CM output: analyses/output/Amil-MirMachine/Mir-988.PRE.result jobid: 1104 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-988.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-988.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:21 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-934.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-934.PRE.gff, analyses/output/Amil-MirMachine/Mir-934.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-934.PRE.unfiltered jobid: 1003 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-934.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-934.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-934.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:21 2023] Finished job 1003. 1416 of 2231 steps (63%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-934.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:21 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-934.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-934.PRE.filtered.gff jobid: 1616 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-934.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-934.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-934.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:21 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-934.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-934.PRE.filtered.fasta jobid: 2175 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-934.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-934.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-934.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:21 2023] Finished job 2175. 1417 of 2231 steps (64%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:21 2023] Finished job 1616. 1418 of 2231 steps (64%) done [Fri Nov 3 10:41:29 2023] Finished job 1104. 1419 of 2231 steps (64%) done [Fri Nov 3 10:41:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4891.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4891.PRE.result jobid: 714 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4891.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4891.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-988.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-988.PRE.gff, analyses/output/Amil-MirMachine/Mir-988.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-988.PRE.unfiltered jobid: 1103 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-988.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-988.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-988.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:29 2023] Finished job 1103. 1420 of 2231 steps (64%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-988.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-988.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-988.PRE.filtered.fasta jobid: 2225 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-988.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-988.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-988.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-988.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-988.PRE.filtered.gff jobid: 1666 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-988.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-988.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-988.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:29 2023] Finished job 2225. 1421 of 2231 steps (64%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:29 2023] Finished job 1666. 1422 of 2231 steps (64%) done [Fri Nov 3 10:41:33 2023] Finished job 714. 1423 of 2231 steps (64%) done [Fri Nov 3 10:41:33 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4891.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4891.PRE.gff, analyses/output/Amil-MirMachine/Mir-4891.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4891.PRE.unfiltered jobid: 713 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4891.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4891.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4891.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:33 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-966.PRE.CM output: analyses/output/Amil-MirMachine/Mir-966.PRE.result jobid: 1044 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-966.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-966.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:33 2023] Finished job 713. 1424 of 2231 steps (64%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4891.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4891.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4891.PRE.filtered.fasta jobid: 2030 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4891.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4891.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4891.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4891.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4891.PRE.filtered.gff jobid: 1471 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4891.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4891.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4891.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:33 2023] Finished job 2030. 1425 of 2231 steps (64%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:33 2023] Finished job 1471. 1426 of 2231 steps (64%) done [Fri Nov 3 10:41:36 2023] Finished job 1044. 1427 of 2231 steps (64%) done [Fri Nov 3 10:41:36 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-966.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-966.PRE.gff, analyses/output/Amil-MirMachine/Mir-966.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-966.PRE.unfiltered jobid: 1043 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-966.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-966.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-966.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:36 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-770.PRE.CM output: analyses/output/Amil-MirMachine/Mir-770.PRE.result jobid: 950 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-770.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-770.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:36 2023] Finished job 1043. 1428 of 2231 steps (64%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-966.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:36 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-966.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-966.PRE.filtered.gff jobid: 1636 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-966.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-966.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-966.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:36 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-966.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-966.PRE.filtered.fasta jobid: 2195 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-966.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-966.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-966.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:37 2023] Finished job 2195. 1429 of 2231 steps (64%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:37 2023] Finished job 1636. 1430 of 2231 steps (64%) done [Fri Nov 3 10:41:41 2023] Finished job 950. 1431 of 2231 steps (64%) done [Fri Nov 3 10:41:41 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9538.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9538.PRE.result jobid: 1016 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9538.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9538.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:41 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-770.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-770.PRE.gff, analyses/output/Amil-MirMachine/Mir-770.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-770.PRE.unfiltered jobid: 949 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-770.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-770.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-770.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:41 2023] Finished job 949. 1432 of 2231 steps (64%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-770.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:41 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-770.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-770.PRE.filtered.fasta jobid: 2148 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-770.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-770.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-770.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:41 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-770.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-770.PRE.filtered.gff jobid: 1589 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-770.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-770.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-770.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:41 2023] Finished job 2148. 1433 of 2231 steps (64%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:41 2023] Finished job 1589. 1434 of 2231 steps (64%) done [Fri Nov 3 10:41:47 2023] Finished job 1016. 1435 of 2231 steps (64%) done [Fri Nov 3 10:41:47 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9538.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9538.PRE.gff, analyses/output/Amil-MirMachine/Mir-9538.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9538.PRE.unfiltered jobid: 1015 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9538.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9538.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9538.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:47 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-483.PRE.CM output: analyses/output/Amil-MirMachine/Mir-483.PRE.result jobid: 656 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-483.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-483.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:47 2023] Finished job 1015. 1436 of 2231 steps (64%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9538.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:48 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9538.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9538.PRE.filtered.fasta jobid: 2181 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9538.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9538.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9538.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:48 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9538.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9538.PRE.filtered.gff jobid: 1622 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9538.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9538.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9538.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:48 2023] Finished job 2181. 1437 of 2231 steps (64%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:48 2023] Finished job 1622. 1438 of 2231 steps (64%) done [Fri Nov 3 10:41:52 2023] Finished job 1010. 1439 of 2231 steps (65%) done [Fri Nov 3 10:41:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7332.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7332.PRE.result jobid: 896 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7332.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7332.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9388.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9388.PRE.gff, analyses/output/Amil-MirMachine/Mir-9388.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9388.PRE.unfiltered jobid: 1009 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9388.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9388.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9388.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:52 2023] Finished job 1009. 1440 of 2231 steps (65%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9388.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9388.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9388.PRE.filtered.gff jobid: 1619 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9388.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9388.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9388.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9388.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9388.PRE.filtered.fasta jobid: 2178 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9388.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9388.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9388.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:53 2023] Finished job 2178. 1441 of 2231 steps (65%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:53 2023] Finished job 1619. 1442 of 2231 steps (65%) done [Fri Nov 3 10:41:56 2023] Finished job 656. 1443 of 2231 steps (65%) done [Fri Nov 3 10:41:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-483.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-483.PRE.gff, analyses/output/Amil-MirMachine/Mir-483.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-483.PRE.unfiltered jobid: 655 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-483.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-483.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-483.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2004.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2004.PRE.result jobid: 266 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2004.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2004.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:56 2023] Finished job 655. 1444 of 2231 steps (65%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-483.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-483.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-483.PRE.filtered.fasta jobid: 2001 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-483.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-483.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-483.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-483.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-483.PRE.filtered.gff jobid: 1442 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-483.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-483.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-483.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:56 2023] Finished job 2001. 1445 of 2231 steps (65%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:57 2023] Finished job 1442. 1446 of 2231 steps (65%) done [Fri Nov 3 10:41:57 2023] Finished job 896. 1447 of 2231 steps (65%) done [Fri Nov 3 10:41:57 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7332.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7332.PRE.gff, analyses/output/Amil-MirMachine/Mir-7332.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7332.PRE.unfiltered jobid: 895 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7332.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7332.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7332.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:57 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3617.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3617.PRE.result jobid: 566 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3617.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3617.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:41:57 2023] Finished job 895. 1448 of 2231 steps (65%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7332.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:41:57 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7332.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7332.PRE.filtered.fasta jobid: 2121 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7332.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7332.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7332.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:57 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7332.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7332.PRE.filtered.gff jobid: 1562 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7332.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7332.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7332.PRE resources: tmpdir=/tmp [Fri Nov 3 10:41:57 2023] Finished job 2121. 1449 of 2231 steps (65%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:41:57 2023] Finished job 1562. 1450 of 2231 steps (65%) done [Fri Nov 3 10:42:01 2023] Finished job 266. 1451 of 2231 steps (65%) done [Fri Nov 3 10:42:01 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2004.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2004.PRE.gff, analyses/output/Amil-MirMachine/Mir-2004.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2004.PRE.unfiltered jobid: 265 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2004.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2004.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2004.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:01 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2796.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2796.PRE.result jobid: 446 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2796.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2796.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:01 2023] Finished job 265. 1452 of 2231 steps (65%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2004.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:01 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2004.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2004.PRE.filtered.fasta jobid: 1806 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2004.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2004.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2004.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:01 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2004.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2004.PRE.filtered.gff jobid: 1247 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2004.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2004.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2004.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:01 2023] Finished job 1806. 1453 of 2231 steps (65%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:01 2023] Finished job 1247. 1454 of 2231 steps (65%) done [Fri Nov 3 10:42:02 2023] Finished job 566. 1455 of 2231 steps (65%) done [Fri Nov 3 10:42:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3617.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3617.PRE.gff, analyses/output/Amil-MirMachine/Mir-3617.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3617.PRE.unfiltered jobid: 565 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3617.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3617.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3617.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4866.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4866.PRE.result jobid: 686 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4866.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4866.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:02 2023] Finished job 565. 1456 of 2231 steps (65%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3617.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3617.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3617.PRE.filtered.fasta jobid: 1956 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3617.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3617.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3617.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3617.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3617.PRE.filtered.gff jobid: 1397 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3617.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3617.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3617.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:02 2023] Finished job 1956. 1457 of 2231 steps (65%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:02 2023] Finished job 1397. 1458 of 2231 steps (65%) done [Fri Nov 3 10:42:05 2023] Finished job 446. 1459 of 2231 steps (65%) done [Fri Nov 3 10:42:05 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2796.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2796.PRE.gff, analyses/output/Amil-MirMachine/Mir-2796.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2796.PRE.unfiltered jobid: 445 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2796.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2796.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2796.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-316.PRE.CM output: analyses/output/Amil-MirMachine/Mir-316.PRE.result jobid: 506 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-316.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-316.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] Finished job 445. 1460 of 2231 steps (65%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2796.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:05 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2796.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2796.PRE.filtered.fasta jobid: 1896 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2796.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2796.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2796.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2796.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2796.PRE.filtered.gff jobid: 1337 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2796.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2796.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2796.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] Finished job 1896. 1461 of 2231 steps (65%) done Select jobs to execute... [Fri Nov 3 10:42:05 2023] Finished job 686. 1462 of 2231 steps (66%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:05 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4866.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4866.PRE.gff, analyses/output/Amil-MirMachine/Mir-4866.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4866.PRE.unfiltered jobid: 685 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4866.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4866.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4866.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-67.PRE.CM output: analyses/output/Amil-MirMachine/Mir-67.PRE.result jobid: 806 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-67.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-67.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] Finished job 1337. 1463 of 2231 steps (66%) done Select jobs to execute... [Fri Nov 3 10:42:05 2023] Finished job 685. 1464 of 2231 steps (66%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4866.PRE.ext.gff. [Fri Nov 3 10:42:05 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4866.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4866.PRE.filtered.fasta jobid: 2016 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4866.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4866.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4866.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4866.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4866.PRE.filtered.gff jobid: 1457 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4866.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4866.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4866.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:05 2023] Finished job 2016. 1465 of 2231 steps (66%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:06 2023] Finished job 1457. 1466 of 2231 steps (66%) done [Fri Nov 3 10:42:12 2023] Finished job 806. 1467 of 2231 steps (66%) done [Fri Nov 3 10:42:12 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12380.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12380.PRE.result jobid: 56 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12380.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12380.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:12 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-67.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-67.PRE.gff, analyses/output/Amil-MirMachine/Mir-67.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-67.PRE.unfiltered jobid: 805 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-67.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-67.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-67.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:13 2023] Finished job 805. 1468 of 2231 steps (66%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-67.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-67.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-67.PRE.filtered.fasta jobid: 2076 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-67.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-67.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-67.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-67.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-67.PRE.filtered.gff jobid: 1517 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-67.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-67.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-67.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:13 2023] Finished job 2076. 1469 of 2231 steps (66%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:13 2023] Finished job 1517. 1470 of 2231 steps (66%) done [Fri Nov 3 10:42:15 2023] Finished job 506. 1471 of 2231 steps (66%) done [Fri Nov 3 10:42:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1677.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1677.PRE.result jobid: 176 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1677.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1677.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-316.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-316.PRE.gff, analyses/output/Amil-MirMachine/Mir-316.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-316.PRE.unfiltered jobid: 505 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-316.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-316.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-316.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:15 2023] Finished job 505. 1472 of 2231 steps (66%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-316.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-316.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-316.PRE.filtered.fasta jobid: 1926 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-316.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-316.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-316.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-316.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-316.PRE.filtered.gff jobid: 1367 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-316.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-316.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-316.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:15 2023] Finished job 1926. 1473 of 2231 steps (66%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:16 2023] Finished job 1367. 1474 of 2231 steps (66%) done [Fri Nov 3 10:42:16 2023] Finished job 56. 1475 of 2231 steps (66%) done [Fri Nov 3 10:42:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12380.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12380.PRE.gff, analyses/output/Amil-MirMachine/Mir-12380.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12380.PRE.unfiltered jobid: 55 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12380.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12380.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12380.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1987.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1987.PRE.result jobid: 236 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1987.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1987.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:16 2023] Finished job 55. 1476 of 2231 steps (66%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12380.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12380.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12380.PRE.filtered.fasta jobid: 1701 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12380.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12380.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12380.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12380.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12380.PRE.filtered.gff jobid: 1142 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12380.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12380.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12380.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:16 2023] Finished job 1701. 1477 of 2231 steps (66%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:16 2023] Finished job 1142. 1478 of 2231 steps (66%) done [Fri Nov 3 10:42:24 2023] Finished job 236. 1479 of 2231 steps (66%) done [Fri Nov 3 10:42:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1987.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1987.PRE.gff, analyses/output/Amil-MirMachine/Mir-1987.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1987.PRE.unfiltered jobid: 235 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1987.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1987.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1987.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2191.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2191.PRE.result jobid: 356 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2191.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2191.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:25 2023] Finished job 235. 1480 of 2231 steps (66%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1987.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1987.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1987.PRE.filtered.fasta jobid: 1791 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1987.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1987.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1987.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1987.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1987.PRE.filtered.gff jobid: 1232 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1987.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1987.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1987.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:25 2023] Finished job 1791. 1481 of 2231 steps (66%) done Select jobs to execute... [Fri Nov 3 10:42:25 2023] Finished job 176. 1482 of 2231 steps (66%) done [Fri Nov 3 10:42:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1677.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1677.PRE.gff, analyses/output/Amil-MirMachine/Mir-1677.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1677.PRE.unfiltered jobid: 175 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1677.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1677.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1677.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-6715.PRE.CM output: analyses/output/Amil-MirMachine/Mir-6715.PRE.result jobid: 812 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6715.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-6715.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:25 2023] Finished job 175. 1483 of 2231 steps (66%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1677.PRE.ext.gff. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:42:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1677.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1677.PRE.filtered.fasta jobid: 1761 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1677.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1677.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1677.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1677.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1677.PRE.filtered.gff jobid: 1202 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1677.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1677.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1677.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:25 2023] Finished job 1761. 1484 of 2231 steps (67%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:25 2023] Finished job 1232. 1485 of 2231 steps (67%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:25 2023] Finished job 1202. 1486 of 2231 steps (67%) done [Fri Nov 3 10:42:28 2023] Finished job 356. 1487 of 2231 steps (67%) done [Fri Nov 3 10:42:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2131.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2131.PRE.result jobid: 338 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2131.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2131.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2191.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2191.PRE.gff, analyses/output/Amil-MirMachine/Mir-2191.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2191.PRE.unfiltered jobid: 355 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2191.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2191.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2191.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:28 2023] Finished job 355. 1488 of 2231 steps (67%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2191.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2191.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2191.PRE.filtered.fasta jobid: 1851 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2191.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2191.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2191.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2191.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2191.PRE.filtered.gff jobid: 1292 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2191.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2191.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2191.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:28 2023] Finished job 1851. 1489 of 2231 steps (67%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:29 2023] Finished job 1292. 1490 of 2231 steps (67%) done [Fri Nov 3 10:42:30 2023] Finished job 812. 1491 of 2231 steps (67%) done [Fri Nov 3 10:42:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-6715.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-6715.PRE.gff, analyses/output/Amil-MirMachine/Mir-6715.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-6715.PRE.unfiltered jobid: 811 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6715.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-6715.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-6715.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-989.PRE.CM output: analyses/output/Amil-MirMachine/Mir-989.PRE.result jobid: 1106 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-989.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-989.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:30 2023] Finished job 811. 1492 of 2231 steps (67%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-6715.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-6715.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-6715.PRE.filtered.fasta jobid: 2079 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6715.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-6715.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-6715.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-6715.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-6715.PRE.filtered.gff jobid: 1520 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-6715.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-6715.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-6715.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:30 2023] Finished job 2079. 1493 of 2231 steps (67%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:30 2023] Finished job 1520. 1494 of 2231 steps (67%) done [Fri Nov 3 10:42:35 2023] Finished job 1106. 1495 of 2231 steps (67%) done [Fri Nov 3 10:42:35 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-989.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-989.PRE.gff, analyses/output/Amil-MirMachine/Mir-989.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-989.PRE.unfiltered jobid: 1105 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-989.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-989.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-989.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:35 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-967.PRE.CM output: analyses/output/Amil-MirMachine/Mir-967.PRE.result jobid: 1046 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-967.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-967.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:35 2023] Finished job 1105. 1496 of 2231 steps (67%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-989.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-989.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-989.PRE.filtered.fasta jobid: 2226 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-989.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-989.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-989.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-989.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-989.PRE.filtered.gff jobid: 1667 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-989.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-989.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-989.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:35 2023] Finished job 2226. 1497 of 2231 steps (67%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:35 2023] Finished job 1667. 1498 of 2231 steps (67%) done [Fri Nov 3 10:42:37 2023] Finished job 338. 1499 of 2231 steps (67%) done [Fri Nov 3 10:42:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2131.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2131.PRE.gff, analyses/output/Amil-MirMachine/Mir-2131.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2131.PRE.unfiltered jobid: 337 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2131.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2131.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2131.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-139.PRE.CM output: analyses/output/Amil-MirMachine/Mir-139.PRE.result jobid: 116 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-139.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-139.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:37 2023] Finished job 337. 1500 of 2231 steps (67%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2131.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2131.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2131.PRE.filtered.fasta jobid: 1842 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2131.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2131.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2131.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2131.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2131.PRE.filtered.gff jobid: 1283 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2131.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2131.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2131.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:37 2023] Finished job 1842. 1501 of 2231 steps (67%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:38 2023] Finished job 1283. 1502 of 2231 steps (67%) done [Fri Nov 3 10:42:38 2023] Finished job 1046. 1503 of 2231 steps (67%) done [Fri Nov 3 10:42:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-194.PRE.CM output: analyses/output/Amil-MirMachine/Mir-194.PRE.result jobid: 220 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-194.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-194.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-967.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-967.PRE.gff, analyses/output/Amil-MirMachine/Mir-967.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-967.PRE.unfiltered jobid: 1045 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-967.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-967.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-967.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:38 2023] Finished job 1045. 1504 of 2231 steps (67%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-967.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-967.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-967.PRE.filtered.fasta jobid: 2196 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-967.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-967.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-967.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-967.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-967.PRE.filtered.gff jobid: 1637 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-967.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-967.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-967.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:38 2023] Finished job 2196. 1505 of 2231 steps (67%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:39 2023] Finished job 1637. 1506 of 2231 steps (68%) done [Fri Nov 3 10:42:41 2023] Finished job 116. 1507 of 2231 steps (68%) done [Fri Nov 3 10:42:41 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-155.PRE.CM output: analyses/output/Amil-MirMachine/Mir-155.PRE.result jobid: 166 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-155.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-155.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:41 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-139.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-139.PRE.gff, analyses/output/Amil-MirMachine/Mir-139.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-139.PRE.unfiltered jobid: 115 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-139.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-139.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-139.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:42 2023] Finished job 115. 1508 of 2231 steps (68%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-139.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-139.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-139.PRE.filtered.fasta jobid: 1731 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-139.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-139.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-139.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-139.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-139.PRE.filtered.gff jobid: 1172 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-139.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-139.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-139.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:42 2023] Finished job 1731. 1509 of 2231 steps (68%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:42 2023] Finished job 1172. 1510 of 2231 steps (68%) done [Fri Nov 3 10:42:44 2023] Finished job 220. 1511 of 2231 steps (68%) done [Fri Nov 3 10:42:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-194.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-194.PRE.gff, analyses/output/Amil-MirMachine/Mir-194.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-194.PRE.unfiltered jobid: 219 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-194.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-194.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-194.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-598.PRE.CM output: analyses/output/Amil-MirMachine/Mir-598.PRE.result jobid: 776 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-598.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-598.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:44 2023] Finished job 219. 1512 of 2231 steps (68%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-194.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-194.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-194.PRE.filtered.fasta jobid: 1783 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-194.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-194.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-194.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-194.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-194.PRE.filtered.gff jobid: 1224 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-194.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-194.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-194.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:44 2023] Finished job 1783. 1513 of 2231 steps (68%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:45 2023] Finished job 1224. 1514 of 2231 steps (68%) done [Fri Nov 3 10:42:48 2023] Finished job 166. 1515 of 2231 steps (68%) done [Fri Nov 3 10:42:48 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-155.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-155.PRE.gff, analyses/output/Amil-MirMachine/Mir-155.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-155.PRE.unfiltered jobid: 165 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-155.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-155.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-155.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:48 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1962.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1962.PRE.result jobid: 226 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1962.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1962.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:48 2023] Finished job 165. 1516 of 2231 steps (68%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-155.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:48 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-155.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-155.PRE.filtered.fasta jobid: 1756 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-155.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-155.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-155.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:48 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-155.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-155.PRE.filtered.gff jobid: 1197 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-155.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-155.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-155.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:48 2023] Finished job 1756. 1517 of 2231 steps (68%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:48 2023] Finished job 1197. 1518 of 2231 steps (68%) done [Fri Nov 3 10:42:50 2023] Finished job 776. 1519 of 2231 steps (68%) done [Fri Nov 3 10:42:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-769.PRE.CM output: analyses/output/Amil-MirMachine/Mir-769.PRE.result jobid: 946 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-769.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-769.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-598.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-598.PRE.gff, analyses/output/Amil-MirMachine/Mir-598.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-598.PRE.unfiltered jobid: 775 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-598.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-598.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-598.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:50 2023] Finished job 775. 1520 of 2231 steps (68%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-598.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-598.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-598.PRE.filtered.fasta jobid: 2061 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-598.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-598.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-598.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-598.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-598.PRE.filtered.gff jobid: 1502 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-598.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-598.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-598.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:50 2023] Finished job 2061. 1521 of 2231 steps (68%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:51 2023] Finished job 1502. 1522 of 2231 steps (68%) done [Fri Nov 3 10:42:52 2023] Finished job 226. 1523 of 2231 steps (68%) done [Fri Nov 3 10:42:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1962.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1962.PRE.gff, analyses/output/Amil-MirMachine/Mir-1962.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1962.PRE.unfiltered jobid: 225 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1962.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1962.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1962.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1379.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1379.PRE.result jobid: 110 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1379.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1379.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:52 2023] Finished job 225. 1524 of 2231 steps (68%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1962.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1962.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1962.PRE.filtered.fasta jobid: 1786 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1962.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1962.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1962.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1962.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1962.PRE.filtered.gff jobid: 1227 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1962.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1962.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1962.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:52 2023] Finished job 1786. 1525 of 2231 steps (68%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:53 2023] Finished job 1227. 1526 of 2231 steps (68%) done [Fri Nov 3 10:42:55 2023] Finished job 946. 1527 of 2231 steps (68%) done [Fri Nov 3 10:42:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-769.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-769.PRE.gff, analyses/output/Amil-MirMachine/Mir-769.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-769.PRE.unfiltered jobid: 945 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-769.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-769.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-769.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-17.PRE.CM output: analyses/output/Amil-MirMachine/Mir-17.PRE.result jobid: 178 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-17.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-17.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:55 2023] Finished job 945. 1528 of 2231 steps (68%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-769.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:42:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-769.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-769.PRE.filtered.fasta jobid: 2146 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-769.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-769.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-769.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-769.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-769.PRE.filtered.gff jobid: 1587 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-769.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-769.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-769.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:55 2023] Finished job 2146. 1529 of 2231 steps (69%) done Select jobs to execute... [Fri Nov 3 10:42:55 2023] Finished job 110. 1530 of 2231 steps (69%) done [Fri Nov 3 10:42:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1379.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1379.PRE.gff, analyses/output/Amil-MirMachine/Mir-1379.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1379.PRE.unfiltered jobid: 109 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1379.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1379.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1379.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-26.PRE.CM output: analyses/output/Amil-MirMachine/Mir-26.PRE.result jobid: 410 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-26.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-26.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:42:55 2023] Finished job 109. 1531 of 2231 steps (69%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1379.PRE.ext.gff. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:42:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1379.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1379.PRE.filtered.fasta jobid: 1728 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1379.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1379.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1379.PRE resources: tmpdir=/tmp [Fri Nov 3 10:42:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1379.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1379.PRE.filtered.gff jobid: 1169 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1379.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1379.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1379.PRE resources: tmpdir=/tmp ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:55 2023] Finished job 1728. 1532 of 2231 steps (69%) done Select jobs to execute... [Fri Nov 3 10:42:55 2023] Finished job 1587. 1533 of 2231 steps (69%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:42:56 2023] Finished job 1169. 1534 of 2231 steps (69%) done [Fri Nov 3 10:43:00 2023] Finished job 178. 1535 of 2231 steps (69%) done [Fri Nov 3 10:43:00 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-17.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-17.PRE.gff, analyses/output/Amil-MirMachine/Mir-17.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-17.PRE.unfiltered jobid: 177 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-17.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-17.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-17.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:00 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1989.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1989.PRE.result jobid: 238 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1989.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1989.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:00 2023] Finished job 177. 1536 of 2231 steps (69%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-17.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:00 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-17.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-17.PRE.filtered.fasta jobid: 1762 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-17.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-17.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-17.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:00 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-17.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-17.PRE.filtered.gff jobid: 1203 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-17.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-17.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-17.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:00 2023] Finished job 1762. 1537 of 2231 steps (69%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:01 2023] Finished job 1203. 1538 of 2231 steps (69%) done [Fri Nov 3 10:43:01 2023] Finished job 410. 1539 of 2231 steps (69%) done [Fri Nov 3 10:43:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-26.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-26.PRE.gff, analyses/output/Amil-MirMachine/Mir-26.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-26.PRE.unfiltered jobid: 409 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-26.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-26.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-26.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-788.PRE.CM output: analyses/output/Amil-MirMachine/Mir-788.PRE.result jobid: 958 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-788.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-788.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:02 2023] Finished job 409. 1540 of 2231 steps (69%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-26.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-26.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-26.PRE.filtered.gff jobid: 1319 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-26.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-26.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-26.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-26.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-26.PRE.filtered.fasta jobid: 1878 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-26.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-26.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-26.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:02 2023] Finished job 1878. 1541 of 2231 steps (69%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:02 2023] Finished job 1319. 1542 of 2231 steps (69%) done [Fri Nov 3 10:43:10 2023] Finished job 238. 1543 of 2231 steps (69%) done [Fri Nov 3 10:43:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1989.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1989.PRE.gff, analyses/output/Amil-MirMachine/Mir-1989.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1989.PRE.unfiltered jobid: 237 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1989.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1989.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1989.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9540.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9540.PRE.result jobid: 1018 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9540.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9540.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:10 2023] Finished job 237. 1544 of 2231 steps (69%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1989.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1989.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1989.PRE.filtered.gff jobid: 1233 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1989.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1989.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1989.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1989.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1989.PRE.filtered.fasta jobid: 1792 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1989.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1989.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1989.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:11 2023] Finished job 1792. 1545 of 2231 steps (69%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:11 2023] Finished job 1233. 1546 of 2231 steps (69%) done [Fri Nov 3 10:43:15 2023] Finished job 1018. 1547 of 2231 steps (69%) done [Fri Nov 3 10:43:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9540.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9540.PRE.gff, analyses/output/Amil-MirMachine/Mir-9540.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9540.PRE.unfiltered jobid: 1017 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9540.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9540.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4830.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4830.PRE.result jobid: 658 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4830.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4830.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:15 2023] Finished job 1017. 1548 of 2231 steps (69%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9540.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9540.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9540.PRE.filtered.fasta jobid: 2182 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9540.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9540.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9540.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9540.PRE.filtered.gff jobid: 1623 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9540.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9540.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9540.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:15 2023] Finished job 2182. 1549 of 2231 steps (69%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:15 2023] Finished job 1623. 1550 of 2231 steps (69%) done [Fri Nov 3 10:43:20 2023] Finished job 958. 1551 of 2231 steps (70%) done [Fri Nov 3 10:43:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-788.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-788.PRE.gff, analyses/output/Amil-MirMachine/Mir-788.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-788.PRE.unfiltered jobid: 957 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-788.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-788.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-788.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7333.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7333.PRE.result jobid: 898 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7333.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7333.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:20 2023] Finished job 957. 1552 of 2231 steps (70%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-788.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-788.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-788.PRE.filtered.gff jobid: 1593 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-788.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-788.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-788.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-788.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-788.PRE.filtered.fasta jobid: 2152 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-788.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-788.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-788.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:20 2023] Finished job 2152. 1553 of 2231 steps (70%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:20 2023] Finished job 1593. 1554 of 2231 steps (70%) done [Fri Nov 3 10:43:22 2023] Finished job 658. 1555 of 2231 steps (70%) done [Fri Nov 3 10:43:22 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4830.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4830.PRE.gff, analyses/output/Amil-MirMachine/Mir-4830.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4830.PRE.unfiltered jobid: 657 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4830.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4830.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4830.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:22 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-599.PRE.CM output: analyses/output/Amil-MirMachine/Mir-599.PRE.result jobid: 778 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-599.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-599.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:22 2023] Finished job 657. 1556 of 2231 steps (70%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4830.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:22 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4830.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4830.PRE.filtered.fasta jobid: 2002 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4830.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4830.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4830.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:22 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4830.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4830.PRE.filtered.gff jobid: 1443 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4830.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4830.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4830.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:22 2023] Finished job 2002. 1557 of 2231 steps (70%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:22 2023] Finished job 1443. 1558 of 2231 steps (70%) done [Fri Nov 3 10:43:24 2023] Finished job 898. 1559 of 2231 steps (70%) done [Fri Nov 3 10:43:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2005.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2005.PRE.result jobid: 268 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2005.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2005.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7333.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7333.PRE.gff, analyses/output/Amil-MirMachine/Mir-7333.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7333.PRE.unfiltered jobid: 897 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7333.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7333.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7333.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:24 2023] Finished job 897. 1560 of 2231 steps (70%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7333.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7333.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7333.PRE.filtered.fasta jobid: 2122 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7333.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7333.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7333.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7333.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7333.PRE.filtered.gff jobid: 1563 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7333.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7333.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7333.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:24 2023] Finished job 2122. 1561 of 2231 steps (70%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:25 2023] Finished job 1563. 1562 of 2231 steps (70%) done [Fri Nov 3 10:43:31 2023] Finished job 268. 1563 of 2231 steps (70%) done [Fri Nov 3 10:43:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-22.PRE.CM output: analyses/output/Amil-MirMachine/Mir-22.PRE.result jobid: 358 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-22.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-22.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2005.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2005.PRE.gff, analyses/output/Amil-MirMachine/Mir-2005.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2005.PRE.unfiltered jobid: 267 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2005.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2005.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2005.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] Finished job 267. 1564 of 2231 steps (70%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2005.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2005.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2005.PRE.filtered.gff jobid: 1248 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2005.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2005.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2005.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2005.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2005.PRE.filtered.fasta jobid: 1807 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2005.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2005.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2005.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] Finished job 1807. 1565 of 2231 steps (70%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:31 2023] Finished job 778. 1566 of 2231 steps (70%) done [Fri Nov 3 10:43:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-317.PRE.CM output: analyses/output/Amil-MirMachine/Mir-317.PRE.result jobid: 508 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-317.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-317.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-599.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-599.PRE.gff, analyses/output/Amil-MirMachine/Mir-599.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-599.PRE.unfiltered jobid: 777 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-599.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-599.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-599.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] Finished job 1248. 1567 of 2231 steps (70%) done Select jobs to execute... [Fri Nov 3 10:43:31 2023] Finished job 777. 1568 of 2231 steps (70%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-599.PRE.ext.gff. [Fri Nov 3 10:43:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-599.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-599.PRE.filtered.fasta jobid: 2062 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-599.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-599.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-599.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-599.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-599.PRE.filtered.gff jobid: 1503 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-599.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-599.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-599.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:31 2023] Finished job 2062. 1569 of 2231 steps (70%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:32 2023] Finished job 1503. 1570 of 2231 steps (70%) done [Fri Nov 3 10:43:36 2023] Finished job 358. 1571 of 2231 steps (70%) done [Fri Nov 3 10:43:36 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-362.PRE.CM output: analyses/output/Amil-MirMachine/Mir-362.PRE.result jobid: 568 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-362.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-362.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:36 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-22.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-22.PRE.gff, analyses/output/Amil-MirMachine/Mir-22.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-22.PRE.unfiltered jobid: 357 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-22.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-22.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-22.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:36 2023] Finished job 357. 1572 of 2231 steps (70%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-22.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:36 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-22.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-22.PRE.filtered.gff jobid: 1293 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-22.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-22.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-22.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:36 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-22.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-22.PRE.filtered.fasta jobid: 1852 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-22.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-22.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-22.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:36 2023] Finished job 1852. 1573 of 2231 steps (71%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:36 2023] Finished job 1293. 1574 of 2231 steps (71%) done [Fri Nov 3 10:43:38 2023] Finished job 508. 1575 of 2231 steps (71%) done [Fri Nov 3 10:43:38 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-28.PRE.CM output: analyses/output/Amil-MirMachine/Mir-28.PRE.result jobid: 448 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-28.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-28.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-317.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-317.PRE.gff, analyses/output/Amil-MirMachine/Mir-317.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-317.PRE.unfiltered jobid: 507 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-317.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-317.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-317.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:38 2023] Finished job 507. 1576 of 2231 steps (71%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-317.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-317.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-317.PRE.filtered.gff jobid: 1368 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-317.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-317.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-317.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-317.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-317.PRE.filtered.fasta jobid: 1927 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-317.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-317.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-317.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:38 2023] Finished job 1927. 1577 of 2231 steps (71%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:39 2023] Finished job 1368. 1578 of 2231 steps (71%) done [Fri Nov 3 10:43:42 2023] Finished job 568. 1579 of 2231 steps (71%) done [Fri Nov 3 10:43:42 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-124.PRE.CM output: analyses/output/Amil-MirMachine/Mir-124.PRE.result jobid: 58 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-124.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-124.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:42 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-362.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-362.PRE.gff, analyses/output/Amil-MirMachine/Mir-362.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-362.PRE.unfiltered jobid: 567 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-362.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-362.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-362.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:42 2023] Finished job 567. 1580 of 2231 steps (71%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-362.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-362.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-362.PRE.filtered.gff jobid: 1398 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-362.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-362.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-362.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-362.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-362.PRE.filtered.fasta jobid: 1957 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-362.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-362.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-362.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:42 2023] Finished job 1957. 1581 of 2231 steps (71%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:43 2023] Finished job 1398. 1582 of 2231 steps (71%) done [Fri Nov 3 10:43:43 2023] Finished job 448. 1583 of 2231 steps (71%) done [Fri Nov 3 10:43:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4869.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4869.PRE.result jobid: 688 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4869.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4869.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-28.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-28.PRE.gff, analyses/output/Amil-MirMachine/Mir-28.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-28.PRE.unfiltered jobid: 447 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-28.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-28.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-28.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:43 2023] Finished job 447. 1584 of 2231 steps (71%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-28.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-28.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-28.PRE.filtered.gff jobid: 1338 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-28.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-28.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-28.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-28.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-28.PRE.filtered.fasta jobid: 1897 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-28.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-28.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-28.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:43 2023] Finished job 1897. 1585 of 2231 steps (71%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:43 2023] Finished job 1338. 1586 of 2231 steps (71%) done [Fri Nov 3 10:43:47 2023] Finished job 58. 1587 of 2231 steps (71%) done [Fri Nov 3 10:43:47 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-124.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-124.PRE.gff, analyses/output/Amil-MirMachine/Mir-124.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-124.PRE.unfiltered jobid: 57 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-124.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-124.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-124.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:47 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-974.PRE.CM output: analyses/output/Amil-MirMachine/Mir-974.PRE.result jobid: 1080 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-974.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-974.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:47 2023] Finished job 57. 1588 of 2231 steps (71%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-124.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:47 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-124.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-124.PRE.filtered.fasta jobid: 1702 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-124.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-124.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-124.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:47 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-124.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-124.PRE.filtered.gff jobid: 1143 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-124.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-124.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-124.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:47 2023] Finished job 1702. 1589 of 2231 steps (71%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:47 2023] Finished job 1143. 1590 of 2231 steps (71%) done [Fri Nov 3 10:43:48 2023] Finished job 688. 1591 of 2231 steps (71%) done [Fri Nov 3 10:43:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-670.PRE.CM output: analyses/output/Amil-MirMachine/Mir-670.PRE.result jobid: 808 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-670.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-670.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4869.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4869.PRE.gff, analyses/output/Amil-MirMachine/Mir-4869.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4869.PRE.unfiltered jobid: 687 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4869.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4869.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4869.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:49 2023] Finished job 687. 1592 of 2231 steps (71%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4869.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4869.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4869.PRE.filtered.gff jobid: 1458 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4869.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4869.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4869.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4869.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4869.PRE.filtered.fasta jobid: 2017 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4869.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4869.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4869.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:49 2023] Finished job 2017. 1593 of 2231 steps (71%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:49 2023] Finished job 1458. 1594 of 2231 steps (71%) done [Fri Nov 3 10:43:56 2023] Finished job 808. 1595 of 2231 steps (71%) done [Fri Nov 3 10:43:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-32.PRE.CM output: analyses/output/Amil-MirMachine/Mir-32.PRE.result jobid: 512 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-32.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-32.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:43:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-670.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-670.PRE.gff, analyses/output/Amil-MirMachine/Mir-670.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-670.PRE.unfiltered jobid: 807 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-670.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-670.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-670.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:57 2023] Finished job 807. 1596 of 2231 steps (72%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-670.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:43:57 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-670.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-670.PRE.filtered.gff jobid: 1518 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-670.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-670.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-670.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:57 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-670.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-670.PRE.filtered.fasta jobid: 2077 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-670.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-670.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-670.PRE resources: tmpdir=/tmp [Fri Nov 3 10:43:57 2023] Finished job 2077. 1597 of 2231 steps (72%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:43:57 2023] Finished job 1518. 1598 of 2231 steps (72%) done [Fri Nov 3 10:44:03 2023] Finished job 512. 1599 of 2231 steps (72%) done [Fri Nov 3 10:44:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-574.PRE.CM output: analyses/output/Amil-MirMachine/Mir-574.PRE.result jobid: 758 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-574.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-574.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-32.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-32.PRE.gff, analyses/output/Amil-MirMachine/Mir-32.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-32.PRE.unfiltered jobid: 511 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-32.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-32.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-32.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:03 2023] Finished job 511. 1600 of 2231 steps (72%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-32.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-32.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-32.PRE.filtered.gff jobid: 1370 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-32.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-32.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-32.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-32.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-32.PRE.filtered.fasta jobid: 1929 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-32.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-32.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-32.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:03 2023] Finished job 1929. 1601 of 2231 steps (72%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:04 2023] Finished job 1370. 1602 of 2231 steps (72%) done [Fri Nov 3 10:44:05 2023] Finished job 1080. 1603 of 2231 steps (72%) done [Fri Nov 3 10:44:05 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-991.PRE.CM output: analyses/output/Amil-MirMachine/Mir-991.PRE.result jobid: 1108 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-991.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-991.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:05 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-974.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-974.PRE.gff, analyses/output/Amil-MirMachine/Mir-974.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-974.PRE.unfiltered jobid: 1079 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-974.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-974.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-974.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:05 2023] Finished job 1079. 1604 of 2231 steps (72%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-974.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:05 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-974.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-974.PRE.filtered.gff jobid: 1654 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-974.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-974.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-974.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:05 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-974.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-974.PRE.filtered.fasta jobid: 2213 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-974.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-974.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-974.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:05 2023] Finished job 2213. 1605 of 2231 steps (72%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:05 2023] Finished job 1654. 1606 of 2231 steps (72%) done [Fri Nov 3 10:44:07 2023] Finished job 758. 1607 of 2231 steps (72%) done [Fri Nov 3 10:44:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-574.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-574.PRE.gff, analyses/output/Amil-MirMachine/Mir-574.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-574.PRE.unfiltered jobid: 757 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-574.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-574.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-574.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9681.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9681.PRE.result jobid: 1048 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9681.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9681.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:07 2023] Finished job 757. 1608 of 2231 steps (72%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-574.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-574.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-574.PRE.filtered.fasta jobid: 2052 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-574.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-574.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-574.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-574.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-574.PRE.filtered.gff jobid: 1493 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-574.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-574.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-574.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:07 2023] Finished job 2052. 1609 of 2231 steps (72%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:07 2023] Finished job 1493. 1610 of 2231 steps (72%) done [Fri Nov 3 10:44:11 2023] Finished job 1048. 1611 of 2231 steps (72%) done [Fri Nov 3 10:44:11 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9681.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9681.PRE.gff, analyses/output/Amil-MirMachine/Mir-9681.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9681.PRE.unfiltered jobid: 1047 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9681.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9681.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9681.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:11 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2984.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2984.PRE.result jobid: 466 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2984.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2984.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:11 2023] Finished job 1047. 1612 of 2231 steps (72%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9681.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9681.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9681.PRE.filtered.gff jobid: 1638 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9681.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9681.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9681.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9681.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9681.PRE.filtered.fasta jobid: 2197 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9681.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9681.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9681.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:11 2023] Finished job 2197. 1613 of 2231 steps (72%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:12 2023] Finished job 1638. 1614 of 2231 steps (72%) done [Fri Nov 3 10:44:17 2023] Finished job 1108. 1615 of 2231 steps (72%) done [Fri Nov 3 10:44:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-991.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-991.PRE.gff, analyses/output/Amil-MirMachine/Mir-991.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-991.PRE.unfiltered jobid: 1107 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-991.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-991.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-991.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4886.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4886.PRE.result jobid: 706 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4886.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4886.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:17 2023] Finished job 1107. 1616 of 2231 steps (72%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-991.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-991.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-991.PRE.filtered.gff jobid: 1668 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-991.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-991.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-991.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-991.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-991.PRE.filtered.fasta jobid: 2227 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-991.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-991.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-991.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:17 2023] Finished job 2227. 1617 of 2231 steps (72%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:17 2023] Finished job 1668. 1618 of 2231 steps (73%) done [Fri Nov 3 10:44:18 2023] Finished job 466. 1619 of 2231 steps (73%) done [Fri Nov 3 10:44:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2014.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2014.PRE.result jobid: 284 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2014.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2014.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2984.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2984.PRE.gff, analyses/output/Amil-MirMachine/Mir-2984.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2984.PRE.unfiltered jobid: 465 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2984.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2984.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:18 2023] Finished job 465. 1620 of 2231 steps (73%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2984.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:18 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2984.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2984.PRE.filtered.fasta jobid: 1906 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2984.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2984.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:18 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2984.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2984.PRE.filtered.gff jobid: 1347 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2984.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2984.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:18 2023] Finished job 1906. 1621 of 2231 steps (73%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:18 2023] Finished job 1347. 1622 of 2231 steps (73%) done [Fri Nov 3 10:44:20 2023] Finished job 706. 1623 of 2231 steps (73%) done [Fri Nov 3 10:44:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1329.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1329.PRE.result jobid: 96 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1329.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1329.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4886.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4886.PRE.gff, analyses/output/Amil-MirMachine/Mir-4886.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4886.PRE.unfiltered jobid: 705 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4886.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4886.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4886.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:20 2023] Finished job 705. 1624 of 2231 steps (73%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4886.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4886.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4886.PRE.filtered.fasta jobid: 2026 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4886.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4886.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4886.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4886.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4886.PRE.filtered.gff jobid: 1467 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4886.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4886.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4886.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:20 2023] Finished job 2026. 1625 of 2231 steps (73%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:20 2023] Finished job 1467. 1626 of 2231 steps (73%) done [Fri Nov 3 10:44:25 2023] Finished job 284. 1627 of 2231 steps (73%) done [Fri Nov 3 10:44:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-384.PRE.CM output: analyses/output/Amil-MirMachine/Mir-384.PRE.result jobid: 582 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-384.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-384.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2014.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2014.PRE.gff, analyses/output/Amil-MirMachine/Mir-2014.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2014.PRE.unfiltered jobid: 283 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2014.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2014.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2014.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:25 2023] Finished job 283. 1628 of 2231 steps (73%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2014.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2014.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2014.PRE.filtered.gff jobid: 1256 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2014.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2014.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2014.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2014.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2014.PRE.filtered.fasta jobid: 1815 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2014.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2014.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2014.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:25 2023] Finished job 1815. 1629 of 2231 steps (73%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:25 2023] Finished job 1256. 1630 of 2231 steps (73%) done [Fri Nov 3 10:44:25 2023] Finished job 96. 1631 of 2231 steps (73%) done [Fri Nov 3 10:44:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4057.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4057.PRE.result jobid: 590 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4057.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4057.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1329.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1329.PRE.gff, analyses/output/Amil-MirMachine/Mir-1329.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1329.PRE.unfiltered jobid: 95 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1329.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1329.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1329.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:26 2023] Finished job 95. 1632 of 2231 steps (73%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1329.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1329.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1329.PRE.filtered.fasta jobid: 1721 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1329.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1329.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1329.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1329.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1329.PRE.filtered.gff jobid: 1162 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1329.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1329.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1329.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:26 2023] Finished job 1721. 1633 of 2231 steps (73%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:26 2023] Finished job 1162. 1634 of 2231 steps (73%) done [Fri Nov 3 10:44:29 2023] Finished job 582. 1635 of 2231 steps (73%) done [Fri Nov 3 10:44:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-384.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-384.PRE.gff, analyses/output/Amil-MirMachine/Mir-384.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-384.PRE.unfiltered jobid: 581 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-384.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-384.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-384.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-255.PRE.CM output: analyses/output/Amil-MirMachine/Mir-255.PRE.result jobid: 402 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-255.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-255.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:29 2023] Finished job 581. 1636 of 2231 steps (73%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-384.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-384.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-384.PRE.filtered.gff jobid: 1405 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-384.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-384.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-384.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-384.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-384.PRE.filtered.fasta jobid: 1964 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-384.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-384.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-384.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:29 2023] Finished job 1964. 1637 of 2231 steps (73%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:30 2023] Finished job 1405. 1638 of 2231 steps (73%) done [Fri Nov 3 10:44:31 2023] Finished job 590. 1639 of 2231 steps (73%) done [Fri Nov 3 10:44:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12.PRE.result jobid: 38 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4057.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4057.PRE.gff, analyses/output/Amil-MirMachine/Mir-4057.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4057.PRE.unfiltered jobid: 589 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4057.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4057.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4057.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:31 2023] Finished job 589. 1640 of 2231 steps (74%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4057.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4057.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4057.PRE.filtered.fasta jobid: 1968 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4057.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4057.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4057.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4057.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4057.PRE.filtered.gff jobid: 1409 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4057.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4057.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4057.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:31 2023] Finished job 1968. 1641 of 2231 steps (74%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:31 2023] Finished job 1409. 1642 of 2231 steps (74%) done [Fri Nov 3 10:44:40 2023] Finished job 402. 1643 of 2231 steps (74%) done [Fri Nov 3 10:44:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12087.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12087.PRE.result jobid: 44 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12087.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12087.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-255.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-255.PRE.gff, analyses/output/Amil-MirMachine/Mir-255.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-255.PRE.unfiltered jobid: 401 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-255.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-255.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-255.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:40 2023] Finished job 401. 1644 of 2231 steps (74%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-255.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-255.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-255.PRE.filtered.fasta jobid: 1874 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-255.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-255.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-255.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-255.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-255.PRE.filtered.gff jobid: 1315 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-255.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-255.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-255.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:40 2023] Finished job 1874. 1645 of 2231 steps (74%) done Select jobs to execute... [Fri Nov 3 10:44:40 2023] Finished job 38. 1646 of 2231 steps (74%) done [Fri Nov 3 10:44:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12.PRE.gff, analyses/output/Amil-MirMachine/Mir-12.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12.PRE.unfiltered jobid: 37 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-997.PRE.CM output: analyses/output/Amil-MirMachine/Mir-997.PRE.result jobid: 1112 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-997.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-997.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:40 2023] Finished job 37. 1647 of 2231 steps (74%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12.PRE.filtered.fasta jobid: 1692 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12.PRE.filtered.gff jobid: 1133 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:44:40 2023] Finished job 1692. 1648 of 2231 steps (74%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:40 2023] Finished job 1315. 1649 of 2231 steps (74%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:41 2023] Finished job 1133. 1650 of 2231 steps (74%) done [Fri Nov 3 10:44:45 2023] Finished job 44. 1651 of 2231 steps (74%) done [Fri Nov 3 10:44:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12087.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12087.PRE.gff, analyses/output/Amil-MirMachine/Mir-12087.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12087.PRE.unfiltered jobid: 43 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12087.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12087.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12087.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-975.PRE.CM output: analyses/output/Amil-MirMachine/Mir-975.PRE.result jobid: 1082 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-975.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-975.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:45 2023] Finished job 43. 1652 of 2231 steps (74%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12087.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12087.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12087.PRE.filtered.gff jobid: 1136 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12087.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12087.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12087.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12087.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12087.PRE.filtered.fasta jobid: 1695 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12087.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12087.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12087.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:45 2023] Finished job 1695. 1653 of 2231 steps (74%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:46 2023] Finished job 1136. 1654 of 2231 steps (74%) done [Fri Nov 3 10:44:51 2023] Finished job 1082. 1655 of 2231 steps (74%) done [Fri Nov 3 10:44:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4766.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4766.PRE.result jobid: 636 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4766.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4766.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-975.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-975.PRE.gff, analyses/output/Amil-MirMachine/Mir-975.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-975.PRE.unfiltered jobid: 1081 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-975.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-975.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-975.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:51 2023] Finished job 1081. 1656 of 2231 steps (74%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-975.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-975.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-975.PRE.filtered.fasta jobid: 2214 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-975.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-975.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-975.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-975.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-975.PRE.filtered.gff jobid: 1655 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-975.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-975.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-975.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:51 2023] Finished job 2214. 1657 of 2231 steps (74%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:52 2023] Finished job 1655. 1658 of 2231 steps (74%) done [Fri Nov 3 10:44:58 2023] Finished job 1112. 1659 of 2231 steps (74%) done [Fri Nov 3 10:44:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-997.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-997.PRE.gff, analyses/output/Amil-MirMachine/Mir-997.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-997.PRE.unfiltered jobid: 1111 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-997.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-997.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-997.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4819.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4819.PRE.result jobid: 642 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4819.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4819.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:58 2023] Finished job 1111. 1660 of 2231 steps (74%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-997.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-997.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-997.PRE.filtered.gff jobid: 1670 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-997.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-997.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-997.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-997.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-997.PRE.filtered.fasta jobid: 2229 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-997.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-997.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-997.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:58 2023] Finished job 2229. 1661 of 2231 steps (74%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:58 2023] Finished job 1670. 1662 of 2231 steps (74%) done [Fri Nov 3 10:44:59 2023] Finished job 636. 1663 of 2231 steps (75%) done [Fri Nov 3 10:44:59 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2008.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2008.PRE.result jobid: 274 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2008.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2008.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:44:59 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4766.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4766.PRE.gff, analyses/output/Amil-MirMachine/Mir-4766.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4766.PRE.unfiltered jobid: 635 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4766.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4766.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4766.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:59 2023] Finished job 635. 1664 of 2231 steps (75%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4766.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:44:59 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4766.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4766.PRE.filtered.fasta jobid: 1991 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4766.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4766.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4766.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:59 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4766.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4766.PRE.filtered.gff jobid: 1432 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4766.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4766.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4766.PRE resources: tmpdir=/tmp [Fri Nov 3 10:44:59 2023] Finished job 1991. 1665 of 2231 steps (75%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:44:59 2023] Finished job 1432. 1666 of 2231 steps (75%) done [Fri Nov 3 10:45:02 2023] Finished job 642. 1667 of 2231 steps (75%) done [Fri Nov 3 10:45:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4819.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4819.PRE.gff, analyses/output/Amil-MirMachine/Mir-4819.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4819.PRE.unfiltered jobid: 641 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4819.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4819.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4819.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-375.PRE.CM output: analyses/output/Amil-MirMachine/Mir-375.PRE.result jobid: 574 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-375.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-375.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:02 2023] Finished job 641. 1668 of 2231 steps (75%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4819.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4819.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4819.PRE.filtered.fasta jobid: 1994 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4819.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4819.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4819.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4819.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4819.PRE.filtered.gff jobid: 1435 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4819.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4819.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4819.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:02 2023] Finished job 1994. 1669 of 2231 steps (75%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:03 2023] Finished job 1435. 1670 of 2231 steps (75%) done [Fri Nov 3 10:45:06 2023] Finished job 274. 1671 of 2231 steps (75%) done [Fri Nov 3 10:45:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2008.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2008.PRE.gff, analyses/output/Amil-MirMachine/Mir-2008.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2008.PRE.unfiltered jobid: 273 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2008.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2008.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2008.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-284.PRE.CM output: analyses/output/Amil-MirMachine/Mir-284.PRE.result jobid: 454 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-284.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-284.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:06 2023] Finished job 273. 1672 of 2231 steps (75%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2008.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2008.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2008.PRE.filtered.gff jobid: 1251 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2008.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2008.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2008.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2008.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2008.PRE.filtered.fasta jobid: 1810 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2008.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2008.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2008.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:06 2023] Finished job 1810. 1673 of 2231 steps (75%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:07 2023] Finished job 1251. 1674 of 2231 steps (75%) done [Fri Nov 3 10:45:09 2023] Finished job 574. 1675 of 2231 steps (75%) done [Fri Nov 3 10:45:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-375.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-375.PRE.gff, analyses/output/Amil-MirMachine/Mir-375.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-375.PRE.unfiltered jobid: 573 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-375.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-375.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-375.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4873.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4873.PRE.result jobid: 694 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4873.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4873.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:09 2023] Finished job 573. 1676 of 2231 steps (75%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-375.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-375.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-375.PRE.filtered.fasta jobid: 1960 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-375.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-375.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-375.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-375.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-375.PRE.filtered.gff jobid: 1401 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-375.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-375.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-375.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:09 2023] Finished job 1960. 1677 of 2231 steps (75%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:09 2023] Finished job 1401. 1678 of 2231 steps (75%) done [Fri Nov 3 10:45:13 2023] Finished job 694. 1679 of 2231 steps (75%) done [Fri Nov 3 10:45:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1992.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1992.PRE.result jobid: 244 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1992.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1992.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4873.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4873.PRE.gff, analyses/output/Amil-MirMachine/Mir-4873.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4873.PRE.unfiltered jobid: 693 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4873.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4873.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4873.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:13 2023] Finished job 693. 1680 of 2231 steps (75%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4873.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4873.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4873.PRE.filtered.fasta jobid: 2020 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4873.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4873.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4873.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4873.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4873.PRE.filtered.gff jobid: 1461 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4873.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4873.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4873.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:13 2023] Finished job 2020. 1681 of 2231 steps (75%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:14 2023] Finished job 1461. 1682 of 2231 steps (75%) done [Fri Nov 3 10:45:15 2023] Finished job 454. 1683 of 2231 steps (75%) done [Fri Nov 3 10:45:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3145.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3145.PRE.result jobid: 500 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3145.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3145.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-284.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-284.PRE.gff, analyses/output/Amil-MirMachine/Mir-284.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-284.PRE.unfiltered jobid: 453 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-284.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-284.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-284.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:15 2023] Finished job 453. 1684 of 2231 steps (75%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-284.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-284.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-284.PRE.filtered.fasta jobid: 1900 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-284.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-284.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-284.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-284.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-284.PRE.filtered.gff jobid: 1341 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-284.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-284.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-284.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:15 2023] Finished job 1900. 1685 of 2231 steps (76%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:15 2023] Finished job 1341. 1686 of 2231 steps (76%) done [Fri Nov 3 10:45:23 2023] Finished job 244. 1687 of 2231 steps (76%) done [Fri Nov 3 10:45:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-36.PRE.CM output: analyses/output/Amil-MirMachine/Mir-36.PRE.result jobid: 560 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-36.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-36.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1992.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1992.PRE.gff, analyses/output/Amil-MirMachine/Mir-1992.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1992.PRE.unfiltered jobid: 243 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1992.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1992.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1992.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:23 2023] Finished job 243. 1688 of 2231 steps (76%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1992.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1992.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1992.PRE.filtered.fasta jobid: 1795 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1992.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1992.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1992.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1992.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1992.PRE.filtered.gff jobid: 1236 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1992.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1992.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1992.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:23 2023] Finished job 1795. 1689 of 2231 steps (76%) done Select jobs to execute... [Fri Nov 3 10:45:23 2023] Finished job 500. 1690 of 2231 steps (76%) done [Fri Nov 3 10:45:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-277.PRE.CM output: analyses/output/Amil-MirMachine/Mir-277.PRE.result jobid: 440 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-277.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-277.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3145.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3145.PRE.gff, analyses/output/Amil-MirMachine/Mir-3145.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3145.PRE.unfiltered jobid: 499 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3145.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-3145.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3145.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:23 2023] Finished job 499. 1691 of 2231 steps (76%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3145.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3145.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3145.PRE.filtered.fasta jobid: 1923 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3145.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3145.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3145.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3145.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3145.PRE.filtered.gff jobid: 1364 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3145.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3145.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3145.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:45:23 2023] Finished job 1923. 1692 of 2231 steps (76%) done Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:23 2023] Finished job 1236. 1693 of 2231 steps (76%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:24 2023] Finished job 1364. 1694 of 2231 steps (76%) done [Fri Nov 3 10:45:27 2023] Finished job 560. 1695 of 2231 steps (76%) done [Fri Nov 3 10:45:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4863.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4863.PRE.result jobid: 680 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4863.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4863.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-36.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-36.PRE.gff, analyses/output/Amil-MirMachine/Mir-36.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-36.PRE.unfiltered jobid: 559 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-36.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-36.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-36.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:27 2023] Finished job 559. 1696 of 2231 steps (76%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-36.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-36.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-36.PRE.filtered.fasta jobid: 1953 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-36.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-36.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-36.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-36.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-36.PRE.filtered.gff jobid: 1394 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-36.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-36.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-36.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:27 2023] Finished job 1953. 1697 of 2231 steps (76%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:28 2023] Finished job 1394. 1698 of 2231 steps (76%) done [Fri Nov 3 10:45:32 2023] Finished job 680. 1699 of 2231 steps (76%) done [Fri Nov 3 10:45:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-653.PRE.CM output: analyses/output/Amil-MirMachine/Mir-653.PRE.result jobid: 800 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-653.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-653.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4863.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4863.PRE.gff, analyses/output/Amil-MirMachine/Mir-4863.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4863.PRE.unfiltered jobid: 679 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4863.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4863.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4863.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:32 2023] Finished job 679. 1700 of 2231 steps (76%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4863.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4863.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4863.PRE.filtered.fasta jobid: 2013 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4863.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4863.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4863.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4863.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4863.PRE.filtered.gff jobid: 1454 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4863.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4863.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4863.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:32 2023] Finished job 2013. 1701 of 2231 steps (76%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:32 2023] Finished job 1454. 1702 of 2231 steps (76%) done [Fri Nov 3 10:45:35 2023] Finished job 440. 1703 of 2231 steps (76%) done [Fri Nov 3 10:45:35 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-326.PRE.CM output: analyses/output/Amil-MirMachine/Mir-326.PRE.result jobid: 522 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-326.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-326.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:35 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-277.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-277.PRE.gff, analyses/output/Amil-MirMachine/Mir-277.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-277.PRE.unfiltered jobid: 439 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-277.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-277.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-277.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:35 2023] Finished job 439. 1704 of 2231 steps (76%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-277.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-277.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-277.PRE.filtered.fasta jobid: 1893 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-277.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-277.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-277.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-277.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-277.PRE.filtered.gff jobid: 1334 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-277.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-277.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-277.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:35 2023] Finished job 1893. 1705 of 2231 steps (76%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:36 2023] Finished job 1334. 1706 of 2231 steps (76%) done [Fri Nov 3 10:45:39 2023] Finished job 522. 1707 of 2231 steps (77%) done [Fri Nov 3 10:45:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2000.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2000.PRE.result jobid: 260 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2000.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2000.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-326.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-326.PRE.gff, analyses/output/Amil-MirMachine/Mir-326.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-326.PRE.unfiltered jobid: 521 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-326.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-326.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-326.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:39 2023] Finished job 521. 1708 of 2231 steps (77%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-326.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-326.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-326.PRE.filtered.fasta jobid: 1934 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-326.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-326.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-326.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-326.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-326.PRE.filtered.gff jobid: 1375 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-326.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-326.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-326.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:39 2023] Finished job 1934. 1709 of 2231 steps (77%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:39 2023] Finished job 1375. 1710 of 2231 steps (77%) done [Fri Nov 3 10:45:41 2023] Finished job 800. 1711 of 2231 steps (77%) done [Fri Nov 3 10:45:41 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9682.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9682.PRE.result jobid: 1050 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9682.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9682.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:41 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-653.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-653.PRE.gff, analyses/output/Amil-MirMachine/Mir-653.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-653.PRE.unfiltered jobid: 799 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-653.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-653.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-653.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:41 2023] Finished job 799. 1712 of 2231 steps (77%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-653.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:41 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-653.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-653.PRE.filtered.fasta jobid: 2073 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-653.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-653.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-653.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:41 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-653.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-653.PRE.filtered.gff jobid: 1514 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-653.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-653.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-653.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:41 2023] Finished job 2073. 1713 of 2231 steps (77%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:41 2023] Finished job 1514. 1714 of 2231 steps (77%) done [Fri Nov 3 10:45:46 2023] Finished job 1050. 1715 of 2231 steps (77%) done [Fri Nov 3 10:45:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9682.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9682.PRE.gff, analyses/output/Amil-MirMachine/Mir-9682.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9682.PRE.unfiltered jobid: 1049 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9682.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9682.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9682.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-374.PRE.CM output: analyses/output/Amil-MirMachine/Mir-374.PRE.result jobid: 572 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-374.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-374.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:46 2023] Finished job 1049. 1716 of 2231 steps (77%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9682.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9682.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9682.PRE.filtered.gff jobid: 1639 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9682.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9682.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9682.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9682.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9682.PRE.filtered.fasta jobid: 2198 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9682.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9682.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9682.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:46 2023] Finished job 2198. 1717 of 2231 steps (77%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:47 2023] Finished job 1639. 1718 of 2231 steps (77%) done [Fri Nov 3 10:45:49 2023] Finished job 260. 1719 of 2231 steps (77%) done [Fri Nov 3 10:45:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7303.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7303.PRE.result jobid: 882 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7303.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7303.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2000.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2000.PRE.gff, analyses/output/Amil-MirMachine/Mir-2000.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2000.PRE.unfiltered jobid: 259 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2000.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2000.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2000.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:49 2023] Finished job 259. 1720 of 2231 steps (77%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2000.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2000.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2000.PRE.filtered.fasta jobid: 1803 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2000.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2000.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2000.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2000.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2000.PRE.filtered.gff jobid: 1244 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2000.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2000.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2000.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:49 2023] Finished job 1803. 1721 of 2231 steps (77%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:50 2023] Finished job 1244. 1722 of 2231 steps (77%) done [Fri Nov 3 10:45:52 2023] Finished job 572. 1723 of 2231 steps (77%) done [Fri Nov 3 10:45:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-374.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-374.PRE.gff, analyses/output/Amil-MirMachine/Mir-374.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-374.PRE.unfiltered jobid: 571 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-374.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-374.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-374.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-969.PRE.CM output: analyses/output/Amil-MirMachine/Mir-969.PRE.result jobid: 1052 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-969.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-969.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:52 2023] Finished job 571. 1724 of 2231 steps (77%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-374.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-374.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-374.PRE.filtered.fasta jobid: 1959 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-374.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-374.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-374.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-374.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-374.PRE.filtered.gff jobid: 1400 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-374.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-374.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-374.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:52 2023] Finished job 1959. 1725 of 2231 steps (77%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:52 2023] Finished job 1400. 1726 of 2231 steps (77%) done [Fri Nov 3 10:45:53 2023] Finished job 882. 1727 of 2231 steps (77%) done [Fri Nov 3 10:45:53 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7303.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7303.PRE.gff, analyses/output/Amil-MirMachine/Mir-7303.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7303.PRE.unfiltered jobid: 881 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7303.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7303.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7303.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:53 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-672.PRE.CM output: analyses/output/Amil-MirMachine/Mir-672.PRE.result jobid: 814 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-672.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-672.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:53 2023] Finished job 881. 1728 of 2231 steps (77%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7303.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7303.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7303.PRE.filtered.fasta jobid: 2114 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7303.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7303.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7303.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7303.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7303.PRE.filtered.gff jobid: 1555 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7303.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7303.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7303.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:53 2023] Finished job 2114. 1729 of 2231 steps (77%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:54 2023] Finished job 1555. 1730 of 2231 steps (78%) done [Fri Nov 3 10:45:57 2023] Finished job 1052. 1731 of 2231 steps (78%) done [Fri Nov 3 10:45:57 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-342.PRE.CM output: analyses/output/Amil-MirMachine/Mir-342.PRE.result jobid: 544 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-342.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-342.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:45:57 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-969.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-969.PRE.gff, analyses/output/Amil-MirMachine/Mir-969.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-969.PRE.unfiltered jobid: 1051 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-969.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-969.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-969.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:57 2023] Finished job 1051. 1732 of 2231 steps (78%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-969.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:45:57 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-969.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-969.PRE.filtered.fasta jobid: 2199 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-969.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-969.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-969.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:57 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-969.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-969.PRE.filtered.gff jobid: 1640 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-969.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-969.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-969.PRE resources: tmpdir=/tmp [Fri Nov 3 10:45:57 2023] Finished job 2199. 1733 of 2231 steps (78%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:45:57 2023] Finished job 1640. 1734 of 2231 steps (78%) done [Fri Nov 3 10:46:03 2023] Finished job 814. 1735 of 2231 steps (78%) done [Fri Nov 3 10:46:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-935.PRE.CM output: analyses/output/Amil-MirMachine/Mir-935.PRE.result jobid: 1006 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-935.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-935.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-672.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-672.PRE.gff, analyses/output/Amil-MirMachine/Mir-672.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-672.PRE.unfiltered jobid: 813 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-672.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-672.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-672.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:03 2023] Finished job 813. 1736 of 2231 steps (78%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-672.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-672.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-672.PRE.filtered.fasta jobid: 2080 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-672.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-672.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-672.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-672.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-672.PRE.filtered.gff jobid: 1521 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-672.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-672.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-672.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:03 2023] Finished job 2080. 1737 of 2231 steps (78%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:03 2023] Finished job 1521. 1738 of 2231 steps (78%) done [Fri Nov 3 10:46:04 2023] Finished job 544. 1739 of 2231 steps (78%) done [Fri Nov 3 10:46:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-999.PRE.CM output: analyses/output/Amil-MirMachine/Mir-999.PRE.result jobid: 1114 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-999.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-999.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-342.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-342.PRE.gff, analyses/output/Amil-MirMachine/Mir-342.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-342.PRE.unfiltered jobid: 543 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-342.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-342.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-342.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:04 2023] Finished job 543. 1740 of 2231 steps (78%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-342.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-342.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-342.PRE.filtered.gff jobid: 1386 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-342.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-342.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-342.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-342.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-342.PRE.filtered.fasta jobid: 1945 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-342.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-342.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-342.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:04 2023] Finished job 1945. 1741 of 2231 steps (78%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:04 2023] Finished job 1386. 1742 of 2231 steps (78%) done [Fri Nov 3 10:46:06 2023] Finished job 1006. 1743 of 2231 steps (78%) done [Fri Nov 3 10:46:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-935.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-935.PRE.gff, analyses/output/Amil-MirMachine/Mir-935.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-935.PRE.unfiltered jobid: 1005 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-935.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-935.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-935.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9690.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9690.PRE.result jobid: 1054 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9690.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9690.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:06 2023] Finished job 1005. 1744 of 2231 steps (78%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-935.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-935.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-935.PRE.filtered.fasta jobid: 2176 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-935.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-935.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-935.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-935.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-935.PRE.filtered.gff jobid: 1617 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-935.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-935.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-935.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:06 2023] Finished job 2176. 1745 of 2231 steps (78%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:06 2023] Finished job 1617. 1746 of 2231 steps (78%) done [Fri Nov 3 10:46:10 2023] Finished job 1054. 1747 of 2231 steps (78%) done [Fri Nov 3 10:46:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-955.PRE.CM output: analyses/output/Amil-MirMachine/Mir-955.PRE.result jobid: 1020 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-955.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-955.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9690.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9690.PRE.gff, analyses/output/Amil-MirMachine/Mir-9690.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9690.PRE.unfiltered jobid: 1053 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9690.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9690.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9690.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:10 2023] Finished job 1053. 1748 of 2231 steps (78%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9690.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9690.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9690.PRE.filtered.fasta jobid: 2200 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9690.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9690.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9690.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9690.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9690.PRE.filtered.gff jobid: 1641 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9690.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9690.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9690.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:10 2023] Finished job 2200. 1749 of 2231 steps (78%) done Select jobs to execute... [Fri Nov 3 10:46:11 2023] Finished job 1114. 1750 of 2231 steps (78%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:46:11 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1541.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1541.PRE.result jobid: 156 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1541.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1541.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:11 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-999.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-999.PRE.gff, analyses/output/Amil-MirMachine/Mir-999.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-999.PRE.unfiltered jobid: 1113 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-999.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-999.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-999.PRE resources: tmpdir=/tmp ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:11 2023] Finished job 1641. 1751 of 2231 steps (78%) done Select jobs to execute... [Fri Nov 3 10:46:11 2023] Finished job 1113. 1752 of 2231 steps (79%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-999.PRE.ext.gff. [Fri Nov 3 10:46:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-999.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-999.PRE.filtered.gff jobid: 1671 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-999.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-999.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-999.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-999.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-999.PRE.filtered.fasta jobid: 2230 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-999.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-999.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-999.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:11 2023] Finished job 2230. 1753 of 2231 steps (79%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:11 2023] Finished job 1671. 1754 of 2231 steps (79%) done [Fri Nov 3 10:46:15 2023] Finished job 156. 1755 of 2231 steps (79%) done [Fri Nov 3 10:46:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-252.PRE.CM output: analyses/output/Amil-MirMachine/Mir-252.PRE.result jobid: 396 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-252.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-252.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1541.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1541.PRE.gff, analyses/output/Amil-MirMachine/Mir-1541.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1541.PRE.unfiltered jobid: 155 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1541.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1541.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:15 2023] Finished job 155. 1756 of 2231 steps (79%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1541.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1541.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1541.PRE.filtered.fasta jobid: 1751 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1541.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1541.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1541.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1541.PRE.filtered.gff jobid: 1192 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1541.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1541.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1541.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:15 2023] Finished job 1751. 1757 of 2231 steps (79%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:15 2023] Finished job 1192. 1758 of 2231 steps (79%) done [Fri Nov 3 10:46:20 2023] Finished job 1020. 1759 of 2231 steps (79%) done [Fri Nov 3 10:46:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-29.PRE.CM output: analyses/output/Amil-MirMachine/Mir-29.PRE.result jobid: 456 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-29.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-29.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-955.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-955.PRE.gff, analyses/output/Amil-MirMachine/Mir-955.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-955.PRE.unfiltered jobid: 1019 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-955.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-955.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-955.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:20 2023] Finished job 1019. 1760 of 2231 steps (79%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-955.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-955.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-955.PRE.filtered.fasta jobid: 2183 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-955.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-955.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-955.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-955.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-955.PRE.filtered.gff jobid: 1624 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-955.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-955.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-955.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:20 2023] Finished job 2183. 1761 of 2231 steps (79%) done Select jobs to execute... [Fri Nov 3 10:46:20 2023] Finished job 396. 1762 of 2231 steps (79%) done [Fri Nov 3 10:46:20 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-673.PRE.CM output: analyses/output/Amil-MirMachine/Mir-673.PRE.result jobid: 816 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-673.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-673.PRE threads: 15 resources: tmpdir=/tmp Building DAG of jobs... [Fri Nov 3 10:46:20 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-252.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-252.PRE.gff, analyses/output/Amil-MirMachine/Mir-252.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-252.PRE.unfiltered jobid: 395 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-252.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-252.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-252.PRE resources: tmpdir=/tmp Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:20 2023] Finished job 395. 1763 of 2231 steps (79%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-252.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:20 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-252.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-252.PRE.filtered.fasta jobid: 1871 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-252.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-252.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-252.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:20 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-252.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-252.PRE.filtered.gff jobid: 1312 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-252.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-252.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-252.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:20 2023] Finished job 1624. 1764 of 2231 steps (79%) done Select jobs to execute... [Fri Nov 3 10:46:20 2023] Finished job 1871. 1765 of 2231 steps (79%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:20 2023] Finished job 1312. 1766 of 2231 steps (79%) done [Fri Nov 3 10:46:25 2023] Finished job 456. 1767 of 2231 steps (79%) done [Fri Nov 3 10:46:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-192.PRE.CM output: analyses/output/Amil-MirMachine/Mir-192.PRE.result jobid: 216 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-192.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-192.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-29.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-29.PRE.gff, analyses/output/Amil-MirMachine/Mir-29.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-29.PRE.unfiltered jobid: 455 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-29.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-29.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-29.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] Finished job 455. 1768 of 2231 steps (79%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-29.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-29.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-29.PRE.filtered.fasta jobid: 1901 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-29.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-29.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-29.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-29.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-29.PRE.filtered.gff jobid: 1342 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-29.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-29.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-29.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] Finished job 816. 1769 of 2231 steps (79%) done Select jobs to execute... [Fri Nov 3 10:46:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-5735.PRE.CM output: analyses/output/Amil-MirMachine/Mir-5735.PRE.result jobid: 756 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5735.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-5735.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-673.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-673.PRE.gff, analyses/output/Amil-MirMachine/Mir-673.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-673.PRE.unfiltered jobid: 815 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-673.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-673.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-673.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] Finished job 1901. 1770 of 2231 steps (79%) done Select jobs to execute... [Fri Nov 3 10:46:25 2023] Finished job 815. 1771 of 2231 steps (79%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-673.PRE.ext.gff. [Fri Nov 3 10:46:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-673.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-673.PRE.filtered.fasta jobid: 2081 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-673.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-673.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-673.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-673.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-673.PRE.filtered.gff jobid: 1522 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-673.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-673.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-673.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:25 2023] Finished job 2081. 1772 of 2231 steps (79%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:25 2023] Finished job 1342. 1773 of 2231 steps (79%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:25 2023] Finished job 1522. 1774 of 2231 steps (80%) done [Fri Nov 3 10:46:31 2023] Finished job 216. 1775 of 2231 steps (80%) done [Fri Nov 3 10:46:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9692.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9692.PRE.result jobid: 1056 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9692.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9692.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-192.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-192.PRE.gff, analyses/output/Amil-MirMachine/Mir-192.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-192.PRE.unfiltered jobid: 215 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-192.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-192.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-192.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:32 2023] Finished job 215. 1776 of 2231 steps (80%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-192.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-192.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-192.PRE.filtered.fasta jobid: 1781 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-192.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-192.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-192.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-192.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-192.PRE.filtered.gff jobid: 1222 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-192.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-192.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-192.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:32 2023] Finished job 1781. 1777 of 2231 steps (80%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:32 2023] Finished job 1222. 1778 of 2231 steps (80%) done [Fri Nov 3 10:46:33 2023] Finished job 756. 1779 of 2231 steps (80%) done [Fri Nov 3 10:46:33 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-133.PRE.CM output: analyses/output/Amil-MirMachine/Mir-133.PRE.result jobid: 98 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-133.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-133.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:33 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-5735.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-5735.PRE.gff, analyses/output/Amil-MirMachine/Mir-5735.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-5735.PRE.unfiltered jobid: 755 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5735.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-5735.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-5735.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:33 2023] Finished job 755. 1780 of 2231 steps (80%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-5735.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-5735.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-5735.PRE.filtered.fasta jobid: 2051 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5735.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-5735.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-5735.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-5735.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-5735.PRE.filtered.gff jobid: 1492 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-5735.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-5735.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-5735.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:33 2023] Finished job 2051. 1781 of 2231 steps (80%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:34 2023] Finished job 1492. 1782 of 2231 steps (80%) done [Fri Nov 3 10:46:36 2023] Finished job 1056. 1783 of 2231 steps (80%) done [Fri Nov 3 10:46:36 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9692.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9692.PRE.gff, analyses/output/Amil-MirMachine/Mir-9692.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9692.PRE.unfiltered jobid: 1055 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9692.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9692.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9692.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:36 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4857.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4857.PRE.result jobid: 668 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4857.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4857.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:36 2023] Finished job 1055. 1784 of 2231 steps (80%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9692.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:36 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9692.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9692.PRE.filtered.fasta jobid: 2201 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9692.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9692.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9692.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:36 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9692.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9692.PRE.filtered.gff jobid: 1642 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9692.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9692.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9692.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:36 2023] Finished job 2201. 1785 of 2231 steps (80%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:36 2023] Finished job 1642. 1786 of 2231 steps (80%) done [Fri Nov 3 10:46:39 2023] Finished job 98. 1787 of 2231 steps (80%) done [Fri Nov 3 10:46:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-133.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-133.PRE.gff, analyses/output/Amil-MirMachine/Mir-133.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-133.PRE.unfiltered jobid: 97 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-133.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-133.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-133.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-324.PRE.CM output: analyses/output/Amil-MirMachine/Mir-324.PRE.result jobid: 518 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-324.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-324.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:40 2023] Finished job 97. 1788 of 2231 steps (80%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-133.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-133.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-133.PRE.filtered.fasta jobid: 1722 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-133.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-133.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-133.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-133.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-133.PRE.filtered.gff jobid: 1163 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-133.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-133.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-133.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:40 2023] Finished job 1722. 1789 of 2231 steps (80%) done Select jobs to execute... [Fri Nov 3 10:46:40 2023] Finished job 668. 1790 of 2231 steps (80%) done [Fri Nov 3 10:46:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2010.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2010.PRE.result jobid: 278 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2010.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2010.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4857.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4857.PRE.gff, analyses/output/Amil-MirMachine/Mir-4857.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4857.PRE.unfiltered jobid: 667 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4857.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4857.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4857.PRE resources: tmpdir=/tmp Building DAG of jobs... [Fri Nov 3 10:46:40 2023] Finished job 667. 1791 of 2231 steps (80%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4857.PRE.ext.gff. Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... Select jobs to execute... [Fri Nov 3 10:46:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4857.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4857.PRE.filtered.gff jobid: 1448 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4857.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4857.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4857.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4857.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4857.PRE.filtered.fasta jobid: 2007 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4857.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4857.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4857.PRE resources: tmpdir=/tmp ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:40 2023] Finished job 2007. 1792 of 2231 steps (80%) done Select jobs to execute... [Fri Nov 3 10:46:40 2023] Finished job 1163. 1793 of 2231 steps (80%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:40 2023] Finished job 1448. 1794 of 2231 steps (80%) done [Fri Nov 3 10:46:42 2023] Finished job 518. 1795 of 2231 steps (80%) done [Fri Nov 3 10:46:42 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-324.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-324.PRE.gff, analyses/output/Amil-MirMachine/Mir-324.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-324.PRE.unfiltered jobid: 517 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-324.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-324.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-324.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:42 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4876.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4876.PRE.result jobid: 698 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4876.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4876.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:42 2023] Finished job 517. 1796 of 2231 steps (81%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-324.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-324.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-324.PRE.filtered.fasta jobid: 1932 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-324.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-324.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-324.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-324.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-324.PRE.filtered.gff jobid: 1373 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-324.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-324.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-324.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:42 2023] Finished job 1932. 1797 of 2231 steps (81%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:43 2023] Finished job 1373. 1798 of 2231 steps (81%) done [Fri Nov 3 10:46:46 2023] Finished job 698. 1799 of 2231 steps (81%) done [Fri Nov 3 10:46:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4876.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4876.PRE.gff, analyses/output/Amil-MirMachine/Mir-4876.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4876.PRE.unfiltered jobid: 697 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4876.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4876.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4876.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4813.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4813.PRE.result jobid: 638 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4813.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4813.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:46 2023] Finished job 697. 1800 of 2231 steps (81%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4876.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4876.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4876.PRE.filtered.fasta jobid: 2022 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4876.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4876.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4876.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4876.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4876.PRE.filtered.gff jobid: 1463 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4876.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4876.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4876.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:46 2023] Finished job 2022. 1801 of 2231 steps (81%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:46 2023] Finished job 1463. 1802 of 2231 steps (81%) done [Fri Nov 3 10:46:49 2023] Finished job 278. 1803 of 2231 steps (81%) done [Fri Nov 3 10:46:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2010.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2010.PRE.gff, analyses/output/Amil-MirMachine/Mir-2010.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2010.PRE.unfiltered jobid: 277 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2010.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2010.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2010.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7293.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7293.PRE.result jobid: 878 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7293.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7293.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:49 2023] Finished job 277. 1804 of 2231 steps (81%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2010.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2010.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2010.PRE.filtered.fasta jobid: 1812 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2010.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2010.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2010.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2010.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2010.PRE.filtered.gff jobid: 1253 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2010.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2010.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2010.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:49 2023] Finished job 1812. 1805 of 2231 steps (81%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:50 2023] Finished job 1253. 1806 of 2231 steps (81%) done [Fri Nov 3 10:46:53 2023] Finished job 878. 1807 of 2231 steps (81%) done [Fri Nov 3 10:46:53 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7293.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7293.PRE.gff, analyses/output/Amil-MirMachine/Mir-7293.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7293.PRE.unfiltered jobid: 877 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7293.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7293.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7293.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:53 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4831.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4831.PRE.result jobid: 660 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4831.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4831.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:53 2023] Finished job 877. 1808 of 2231 steps (81%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7293.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:53 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7293.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7293.PRE.filtered.fasta jobid: 2112 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7293.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7293.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7293.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:53 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7293.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7293.PRE.filtered.gff jobid: 1553 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7293.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7293.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7293.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:53 2023] Finished job 2112. 1809 of 2231 steps (81%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:53 2023] Finished job 1553. 1810 of 2231 steps (81%) done [Fri Nov 3 10:46:55 2023] Finished job 638. 1811 of 2231 steps (81%) done [Fri Nov 3 10:46:55 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4813.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4813.PRE.gff, analyses/output/Amil-MirMachine/Mir-4813.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4813.PRE.unfiltered jobid: 637 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4813.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4813.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4813.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:55 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7463.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7463.PRE.result jobid: 938 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7463.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7463.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:46:55 2023] Finished job 637. 1812 of 2231 steps (81%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4813.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:46:55 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4813.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4813.PRE.filtered.fasta jobid: 1992 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4813.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4813.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4813.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:55 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4813.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4813.PRE.filtered.gff jobid: 1433 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4813.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4813.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4813.PRE resources: tmpdir=/tmp [Fri Nov 3 10:46:55 2023] Finished job 1992. 1813 of 2231 steps (81%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:46:56 2023] Finished job 1433. 1814 of 2231 steps (81%) done [Fri Nov 3 10:47:00 2023] Finished job 938. 1815 of 2231 steps (81%) done [Fri Nov 3 10:47:00 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7463.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7463.PRE.gff, analyses/output/Amil-MirMachine/Mir-7463.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7463.PRE.unfiltered jobid: 937 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7463.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7463.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7463.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:00 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9696.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9696.PRE.result jobid: 1058 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9696.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9696.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:00 2023] Finished job 937. 1816 of 2231 steps (81%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7463.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:00 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7463.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7463.PRE.filtered.fasta jobid: 2142 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7463.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7463.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7463.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:00 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7463.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7463.PRE.filtered.gff jobid: 1583 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7463.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7463.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7463.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:00 2023] Finished job 2142. 1817 of 2231 steps (81%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:00 2023] Finished job 1583. 1818 of 2231 steps (81%) done [Fri Nov 3 10:47:03 2023] Finished job 660. 1819 of 2231 steps (82%) done [Fri Nov 3 10:47:03 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-978.PRE.CM output: analyses/output/Amil-MirMachine/Mir-978.PRE.result jobid: 1088 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-978.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-978.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:03 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4831.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4831.PRE.gff, analyses/output/Amil-MirMachine/Mir-4831.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4831.PRE.unfiltered jobid: 659 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4831.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4831.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4831.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:03 2023] Finished job 659. 1820 of 2231 steps (82%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4831.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:03 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4831.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4831.PRE.filtered.fasta jobid: 2003 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4831.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4831.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4831.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:03 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4831.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4831.PRE.filtered.gff jobid: 1444 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4831.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4831.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4831.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:03 2023] Finished job 2003. 1821 of 2231 steps (82%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:03 2023] Finished job 1444. 1822 of 2231 steps (82%) done [Fri Nov 3 10:47:04 2023] Finished job 1058. 1823 of 2231 steps (82%) done [Fri Nov 3 10:47:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9696.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9696.PRE.gff, analyses/output/Amil-MirMachine/Mir-9696.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9696.PRE.unfiltered jobid: 1057 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9696.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9696.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9696.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-576.PRE.CM output: analyses/output/Amil-MirMachine/Mir-576.PRE.result jobid: 760 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-576.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-576.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:05 2023] Finished job 1057. 1824 of 2231 steps (82%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9696.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:05 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9696.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9696.PRE.filtered.fasta jobid: 2202 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9696.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9696.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9696.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:05 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9696.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9696.PRE.filtered.gff jobid: 1643 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9696.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9696.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9696.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:05 2023] Finished job 2202. 1825 of 2231 steps (82%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:05 2023] Finished job 1643. 1826 of 2231 steps (82%) done [Fri Nov 3 10:47:07 2023] Finished job 1088. 1827 of 2231 steps (82%) done [Fri Nov 3 10:47:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2011.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2011.PRE.result jobid: 280 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2011.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2011.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-978.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-978.PRE.gff, analyses/output/Amil-MirMachine/Mir-978.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-978.PRE.unfiltered jobid: 1087 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-978.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-978.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-978.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:07 2023] Finished job 1087. 1828 of 2231 steps (82%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-978.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-978.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-978.PRE.filtered.gff jobid: 1658 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-978.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-978.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-978.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-978.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-978.PRE.filtered.fasta jobid: 2217 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-978.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-978.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-978.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:07 2023] Finished job 2217. 1829 of 2231 steps (82%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:07 2023] Finished job 1658. 1830 of 2231 steps (82%) done [Fri Nov 3 10:47:10 2023] Finished job 760. 1831 of 2231 steps (82%) done [Fri Nov 3 10:47:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-576.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-576.PRE.gff, analyses/output/Amil-MirMachine/Mir-576.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-576.PRE.unfiltered jobid: 759 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-576.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-576.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-576.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-325.PRE.CM output: analyses/output/Amil-MirMachine/Mir-325.PRE.result jobid: 520 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-325.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-325.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:10 2023] Finished job 759. 1832 of 2231 steps (82%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-576.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-576.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-576.PRE.filtered.fasta jobid: 2053 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-576.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-576.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-576.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-576.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-576.PRE.filtered.gff jobid: 1494 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-576.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-576.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-576.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:10 2023] Finished job 2053. 1833 of 2231 steps (82%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:10 2023] Finished job 1494. 1834 of 2231 steps (82%) done [Fri Nov 3 10:47:14 2023] Finished job 280. 1835 of 2231 steps (82%) done [Fri Nov 3 10:47:14 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2011.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2011.PRE.gff, analyses/output/Amil-MirMachine/Mir-2011.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2011.PRE.unfiltered jobid: 279 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2011.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2011.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2011.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:14 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-96.PRE.CM output: analyses/output/Amil-MirMachine/Mir-96.PRE.result jobid: 1028 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-96.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-96.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:14 2023] Finished job 279. 1836 of 2231 steps (82%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2011.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2011.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2011.PRE.filtered.fasta jobid: 1813 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2011.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2011.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2011.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2011.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2011.PRE.filtered.gff jobid: 1254 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2011.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2011.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2011.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:14 2023] Finished job 1813. 1837 of 2231 steps (82%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:14 2023] Finished job 1254. 1838 of 2231 steps (82%) done [Fri Nov 3 10:47:19 2023] Finished job 520. 1839 of 2231 steps (82%) done [Fri Nov 3 10:47:19 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-325.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-325.PRE.gff, analyses/output/Amil-MirMachine/Mir-325.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-325.PRE.unfiltered jobid: 519 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-325.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-325.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-325.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:19 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-383.PRE.CM output: analyses/output/Amil-MirMachine/Mir-383.PRE.result jobid: 580 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-383.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-383.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:19 2023] Finished job 519. 1840 of 2231 steps (82%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-325.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:19 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-325.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-325.PRE.filtered.fasta jobid: 1933 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-325.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-325.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-325.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:19 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-325.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-325.PRE.filtered.gff jobid: 1374 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-325.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-325.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-325.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:19 2023] Finished job 1933. 1841 of 2231 steps (83%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:20 2023] Finished job 1374. 1842 of 2231 steps (83%) done [Fri Nov 3 10:47:22 2023] Finished job 1028. 1843 of 2231 steps (83%) done [Fri Nov 3 10:47:22 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-296.PRE.CM output: analyses/output/Amil-MirMachine/Mir-296.PRE.result jobid: 460 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-296.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-296.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:22 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-96.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-96.PRE.gff, analyses/output/Amil-MirMachine/Mir-96.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-96.PRE.unfiltered jobid: 1027 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-96.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-96.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-96.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:22 2023] Finished job 1027. 1844 of 2231 steps (83%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-96.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:22 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-96.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-96.PRE.filtered.gff jobid: 1628 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-96.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-96.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-96.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:22 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-96.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-96.PRE.filtered.fasta jobid: 2187 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-96.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-96.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-96.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:22 2023] Finished job 2187. 1845 of 2231 steps (83%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:22 2023] Finished job 1628. 1846 of 2231 steps (83%) done [Fri Nov 3 10:47:25 2023] Finished job 580. 1847 of 2231 steps (83%) done [Fri Nov 3 10:47:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-383.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-383.PRE.gff, analyses/output/Amil-MirMachine/Mir-383.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-383.PRE.unfiltered jobid: 579 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-383.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-383.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-383.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-675.PRE.CM output: analyses/output/Amil-MirMachine/Mir-675.PRE.result jobid: 820 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-675.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-675.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:25 2023] Finished job 579. 1848 of 2231 steps (83%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-383.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-383.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-383.PRE.filtered.fasta jobid: 1963 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-383.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-383.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-383.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-383.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-383.PRE.filtered.gff jobid: 1404 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-383.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-383.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-383.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:25 2023] Finished job 1963. 1849 of 2231 steps (83%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:25 2023] Finished job 1404. 1850 of 2231 steps (83%) done [Fri Nov 3 10:47:26 2023] Finished job 460. 1851 of 2231 steps (83%) done [Fri Nov 3 10:47:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-296.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-296.PRE.gff, analyses/output/Amil-MirMachine/Mir-296.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-296.PRE.unfiltered jobid: 459 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-296.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-296.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-296.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4879.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4879.PRE.result jobid: 700 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4879.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4879.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:26 2023] Finished job 459. 1852 of 2231 steps (83%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-296.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-296.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-296.PRE.filtered.fasta jobid: 1903 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-296.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-296.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-296.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-296.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-296.PRE.filtered.gff jobid: 1344 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-296.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-296.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-296.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:26 2023] Finished job 1903. 1853 of 2231 steps (83%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:27 2023] Finished job 1344. 1854 of 2231 steps (83%) done [Fri Nov 3 10:47:28 2023] Finished job 820. 1855 of 2231 steps (83%) done [Fri Nov 3 10:47:28 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2582.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2582.PRE.result jobid: 404 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2582.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2582.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:28 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-675.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-675.PRE.gff, analyses/output/Amil-MirMachine/Mir-675.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-675.PRE.unfiltered jobid: 819 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-675.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-675.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-675.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:28 2023] Finished job 819. 1856 of 2231 steps (83%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-675.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:28 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-675.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-675.PRE.filtered.fasta jobid: 2083 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-675.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-675.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-675.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:28 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-675.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-675.PRE.filtered.gff jobid: 1524 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-675.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-675.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-675.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:28 2023] Finished job 2083. 1857 of 2231 steps (83%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:28 2023] Finished job 1524. 1858 of 2231 steps (83%) done [Fri Nov 3 10:47:30 2023] Finished job 700. 1859 of 2231 steps (83%) done [Fri Nov 3 10:47:30 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-135.PRE.CM output: analyses/output/Amil-MirMachine/Mir-135.PRE.result jobid: 104 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-135.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-135.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:30 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4879.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4879.PRE.gff, analyses/output/Amil-MirMachine/Mir-4879.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4879.PRE.unfiltered jobid: 699 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4879.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4879.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4879.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:30 2023] Finished job 699. 1860 of 2231 steps (83%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4879.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4879.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4879.PRE.filtered.fasta jobid: 2023 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4879.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4879.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4879.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4879.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4879.PRE.filtered.gff jobid: 1464 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4879.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4879.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4879.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:30 2023] Finished job 2023. 1861 of 2231 steps (83%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:30 2023] Finished job 1464. 1862 of 2231 steps (83%) done [Fri Nov 3 10:47:37 2023] Finished job 404. 1863 of 2231 steps (84%) done [Fri Nov 3 10:47:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-605.PRE.CM output: analyses/output/Amil-MirMachine/Mir-605.PRE.result jobid: 780 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-605.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-605.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2582.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2582.PRE.gff, analyses/output/Amil-MirMachine/Mir-2582.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2582.PRE.unfiltered jobid: 403 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2582.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2582.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2582.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:37 2023] Finished job 403. 1864 of 2231 steps (84%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2582.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2582.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2582.PRE.filtered.gff jobid: 1316 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2582.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2582.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2582.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2582.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2582.PRE.filtered.fasta jobid: 1875 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2582.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2582.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2582.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:37 2023] Finished job 1875. 1865 of 2231 steps (84%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:38 2023] Finished job 1316. 1866 of 2231 steps (84%) done [Fri Nov 3 10:47:39 2023] Finished job 104. 1867 of 2231 steps (84%) done [Fri Nov 3 10:47:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-370.PRE.CM output: analyses/output/Amil-MirMachine/Mir-370.PRE.result jobid: 570 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-370.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-370.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-135.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-135.PRE.gff, analyses/output/Amil-MirMachine/Mir-135.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-135.PRE.unfiltered jobid: 103 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-135.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-135.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-135.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:39 2023] Finished job 103. 1868 of 2231 steps (84%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-135.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-135.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-135.PRE.filtered.gff jobid: 1166 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-135.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-135.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-135.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-135.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-135.PRE.filtered.fasta jobid: 1725 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-135.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-135.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-135.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:39 2023] Finished job 1725. 1869 of 2231 steps (84%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:39 2023] Finished job 1166. 1870 of 2231 steps (84%) done [Fri Nov 3 10:47:42 2023] Finished job 570. 1871 of 2231 steps (84%) done [Fri Nov 3 10:47:42 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-370.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-370.PRE.gff, analyses/output/Amil-MirMachine/Mir-370.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-370.PRE.unfiltered jobid: 569 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-370.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-370.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-370.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:42 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4859.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4859.PRE.result jobid: 670 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4859.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4859.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:42 2023] Finished job 569. 1872 of 2231 steps (84%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-370.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-370.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-370.PRE.filtered.gff jobid: 1399 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-370.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-370.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-370.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-370.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-370.PRE.filtered.fasta jobid: 1958 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-370.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-370.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-370.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:42 2023] Finished job 1958. 1873 of 2231 steps (84%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:42 2023] Finished job 1399. 1874 of 2231 steps (84%) done [Fri Nov 3 10:47:43 2023] Finished job 780. 1875 of 2231 steps (84%) done [Fri Nov 3 10:47:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-750.PRE.CM output: analyses/output/Amil-MirMachine/Mir-750.PRE.result jobid: 940 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-750.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-750.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-605.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-605.PRE.gff, analyses/output/Amil-MirMachine/Mir-605.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-605.PRE.unfiltered jobid: 779 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-605.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-605.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-605.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:43 2023] Finished job 779. 1876 of 2231 steps (84%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-605.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-605.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-605.PRE.filtered.fasta jobid: 2063 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-605.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-605.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-605.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-605.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-605.PRE.filtered.gff jobid: 1504 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-605.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-605.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-605.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:43 2023] Finished job 2063. 1877 of 2231 steps (84%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:43 2023] Finished job 1504. 1878 of 2231 steps (84%) done [Fri Nov 3 10:47:45 2023] Finished job 670. 1879 of 2231 steps (84%) done [Fri Nov 3 10:47:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-281.PRE.CM output: analyses/output/Amil-MirMachine/Mir-281.PRE.result jobid: 450 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-281.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-281.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4859.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4859.PRE.gff, analyses/output/Amil-MirMachine/Mir-4859.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4859.PRE.unfiltered jobid: 669 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4859.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4859.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4859.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:45 2023] Finished job 669. 1880 of 2231 steps (84%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4859.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4859.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4859.PRE.filtered.gff jobid: 1449 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4859.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4859.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4859.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4859.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4859.PRE.filtered.fasta jobid: 2008 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4859.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4859.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4859.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:45 2023] Finished job 2008. 1881 of 2231 steps (84%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:45 2023] Finished job 1449. 1882 of 2231 steps (84%) done [Fri Nov 3 10:47:50 2023] Finished job 940. 1883 of 2231 steps (84%) done [Fri Nov 3 10:47:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-750.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-750.PRE.gff, analyses/output/Amil-MirMachine/Mir-750.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-750.PRE.unfiltered jobid: 939 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-750.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-750.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-750.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-214.PRE.CM output: analyses/output/Amil-MirMachine/Mir-214.PRE.result jobid: 340 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-214.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-214.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:50 2023] Finished job 939. 1884 of 2231 steps (84%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-750.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-750.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-750.PRE.filtered.fasta jobid: 2143 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-750.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-750.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-750.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-750.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-750.PRE.filtered.gff jobid: 1584 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-750.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-750.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-750.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:50 2023] Finished job 2143. 1885 of 2231 steps (84%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:51 2023] Finished job 1584. 1886 of 2231 steps (85%) done [Fri Nov 3 10:47:51 2023] Finished job 450. 1887 of 2231 steps (85%) done [Fri Nov 3 10:47:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-281.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-281.PRE.gff, analyses/output/Amil-MirMachine/Mir-281.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-281.PRE.unfiltered jobid: 449 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-281.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-281.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-281.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-64.PRE.CM output: analyses/output/Amil-MirMachine/Mir-64.PRE.result jobid: 790 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-64.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-64.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:51 2023] Finished job 449. 1888 of 2231 steps (85%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-281.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-281.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-281.PRE.filtered.gff jobid: 1339 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-281.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-281.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-281.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-281.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-281.PRE.filtered.fasta jobid: 1898 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-281.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-281.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-281.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:52 2023] Finished job 1898. 1889 of 2231 steps (85%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:52 2023] Finished job 1339. 1890 of 2231 steps (85%) done [Fri Nov 3 10:47:56 2023] Finished job 340. 1891 of 2231 steps (85%) done [Fri Nov 3 10:47:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-214.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-214.PRE.gff, analyses/output/Amil-MirMachine/Mir-214.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-214.PRE.unfiltered jobid: 339 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-214.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-214.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-214.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-12085.PRE.CM output: analyses/output/Amil-MirMachine/Mir-12085.PRE.result jobid: 40 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12085.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-12085.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] Finished job 339. 1892 of 2231 steps (85%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-214.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-214.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-214.PRE.filtered.fasta jobid: 1843 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-214.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-214.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-214.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-214.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-214.PRE.filtered.gff jobid: 1284 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-214.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-214.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-214.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] Finished job 1843. 1893 of 2231 steps (85%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:56 2023] Finished job 1284. 1894 of 2231 steps (85%) done [Fri Nov 3 10:47:56 2023] Finished job 790. 1895 of 2231 steps (85%) done [Fri Nov 3 10:47:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-254.PRE.CM output: analyses/output/Amil-MirMachine/Mir-254.PRE.result jobid: 400 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-254.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-254.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-64.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-64.PRE.gff, analyses/output/Amil-MirMachine/Mir-64.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-64.PRE.unfiltered jobid: 789 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-64.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-64.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-64.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] Finished job 789. 1896 of 2231 steps (85%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-64.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-64.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-64.PRE.filtered.gff jobid: 1509 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-64.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-64.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-64.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-64.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-64.PRE.filtered.fasta jobid: 2068 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-64.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-64.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-64.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:56 2023] Finished job 2068. 1897 of 2231 steps (85%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:57 2023] Finished job 1509. 1898 of 2231 steps (85%) done [Fri Nov 3 10:47:58 2023] Finished job 40. 1899 of 2231 steps (85%) done [Fri Nov 3 10:47:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-12085.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-12085.PRE.gff, analyses/output/Amil-MirMachine/Mir-12085.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-12085.PRE.unfiltered jobid: 39 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12085.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12085.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-12085.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-929.PRE.CM output: analyses/output/Amil-MirMachine/Mir-929.PRE.result jobid: 1000 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-929.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-929.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:47:58 2023] Finished job 39. 1900 of 2231 steps (85%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-12085.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:47:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-12085.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12085.PRE.filtered.fasta jobid: 1693 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12085.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12085.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12085.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-12085.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-12085.PRE.filtered.gff jobid: 1134 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-12085.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-12085.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-12085.PRE resources: tmpdir=/tmp [Fri Nov 3 10:47:58 2023] Finished job 1693. 1901 of 2231 steps (85%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:47:59 2023] Finished job 1134. 1902 of 2231 steps (85%) done [Fri Nov 3 10:48:04 2023] Finished job 1000. 1903 of 2231 steps (85%) done [Fri Nov 3 10:48:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-929.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-929.PRE.gff, analyses/output/Amil-MirMachine/Mir-929.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-929.PRE.unfiltered jobid: 999 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-929.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-929.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-929.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9698.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9698.PRE.result jobid: 1060 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9698.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9698.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] Finished job 999. 1904 of 2231 steps (85%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-929.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-929.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-929.PRE.filtered.fasta jobid: 2173 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-929.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-929.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-929.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-929.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-929.PRE.filtered.gff jobid: 1614 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-929.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-929.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-929.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] Finished job 400. 1905 of 2231 steps (85%) done Select jobs to execute... [Fri Nov 3 10:48:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-254.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-254.PRE.gff, analyses/output/Amil-MirMachine/Mir-254.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-254.PRE.unfiltered jobid: 399 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-254.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-254.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-254.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-960.PRE.CM output: analyses/output/Amil-MirMachine/Mir-960.PRE.result jobid: 1030 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-960.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-960.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] Finished job 2173. 1906 of 2231 steps (85%) done Select jobs to execute... [Fri Nov 3 10:48:04 2023] Finished job 399. 1907 of 2231 steps (85%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-254.PRE.ext.gff. [Fri Nov 3 10:48:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-254.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-254.PRE.filtered.fasta jobid: 1873 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-254.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-254.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-254.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-254.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-254.PRE.filtered.gff jobid: 1314 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-254.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-254.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-254.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:04 2023] Finished job 1873. 1908 of 2231 steps (86%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:04 2023] Finished job 1614. 1909 of 2231 steps (86%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:04 2023] Finished job 1314. 1910 of 2231 steps (86%) done [Fri Nov 3 10:48:07 2023] Finished job 1060. 1911 of 2231 steps (86%) done [Fri Nov 3 10:48:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9698.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9698.PRE.gff, analyses/output/Amil-MirMachine/Mir-9698.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9698.PRE.unfiltered jobid: 1059 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9698.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-9698.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9698.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-982.PRE.CM output: analyses/output/Amil-MirMachine/Mir-982.PRE.result jobid: 1090 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-982.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-982.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:07 2023] Finished job 1059. 1912 of 2231 steps (86%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9698.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9698.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9698.PRE.filtered.fasta jobid: 2203 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9698.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9698.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9698.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9698.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9698.PRE.filtered.gff jobid: 1644 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9698.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9698.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9698.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:07 2023] Finished job 2203. 1913 of 2231 steps (86%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:07 2023] Finished job 1644. 1914 of 2231 steps (86%) done [Fri Nov 3 10:48:10 2023] Finished job 1030. 1915 of 2231 steps (86%) done [Fri Nov 3 10:48:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-253.PRE.CM output: analyses/output/Amil-MirMachine/Mir-253.PRE.result jobid: 398 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-253.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-253.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-960.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-960.PRE.gff, analyses/output/Amil-MirMachine/Mir-960.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-960.PRE.unfiltered jobid: 1029 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-960.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-960.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-960.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:10 2023] Finished job 1029. 1916 of 2231 steps (86%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-960.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-960.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-960.PRE.filtered.gff jobid: 1629 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-960.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-960.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-960.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-960.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-960.PRE.filtered.fasta jobid: 2188 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-960.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-960.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-960.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:10 2023] Finished job 2188. 1917 of 2231 steps (86%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:10 2023] Finished job 1629. 1918 of 2231 steps (86%) done [Fri Nov 3 10:48:16 2023] Finished job 398. 1919 of 2231 steps (86%) done [Fri Nov 3 10:48:16 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-253.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-253.PRE.gff, analyses/output/Amil-MirMachine/Mir-253.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-253.PRE.unfiltered jobid: 397 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-253.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-253.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-253.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:16 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-488.PRE.CM output: analyses/output/Amil-MirMachine/Mir-488.PRE.result jobid: 702 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-488.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-488.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:16 2023] Finished job 397. 1920 of 2231 steps (86%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-253.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:16 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-253.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-253.PRE.filtered.fasta jobid: 1872 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-253.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-253.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-253.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:16 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-253.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-253.PRE.filtered.gff jobid: 1313 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-253.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-253.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-253.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:16 2023] Finished job 1872. 1921 of 2231 steps (86%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:17 2023] Finished job 1313. 1922 of 2231 steps (86%) done [Fri Nov 3 10:48:25 2023] Finished job 1090. 1923 of 2231 steps (86%) done [Fri Nov 3 10:48:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-985.PRE.CM output: analyses/output/Amil-MirMachine/Mir-985.PRE.result jobid: 1096 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-985.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-985.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-982.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-982.PRE.gff, analyses/output/Amil-MirMachine/Mir-982.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-982.PRE.unfiltered jobid: 1089 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-982.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-982.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-982.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:25 2023] Finished job 1089. 1924 of 2231 steps (86%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-982.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:25 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-982.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-982.PRE.filtered.gff jobid: 1659 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-982.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-982.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-982.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:25 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-982.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-982.PRE.filtered.fasta jobid: 2218 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-982.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-982.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-982.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:25 2023] Finished job 2218. 1925 of 2231 steps (86%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:25 2023] Finished job 1659. 1926 of 2231 steps (86%) done [Fri Nov 3 10:48:27 2023] Finished job 702. 1927 of 2231 steps (86%) done [Fri Nov 3 10:48:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-962.PRE.CM output: analyses/output/Amil-MirMachine/Mir-962.PRE.result jobid: 1036 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-962.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-962.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-488.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-488.PRE.gff, analyses/output/Amil-MirMachine/Mir-488.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-488.PRE.unfiltered jobid: 701 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-488.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-488.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-488.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:27 2023] Finished job 701. 1928 of 2231 steps (86%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-488.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-488.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-488.PRE.filtered.gff jobid: 1465 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-488.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-488.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-488.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-488.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-488.PRE.filtered.fasta jobid: 2024 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-488.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-488.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-488.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:27 2023] Finished job 2024. 1929 of 2231 steps (86%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:28 2023] Finished job 1465. 1930 of 2231 steps (87%) done [Fri Nov 3 10:48:29 2023] Finished job 1096. 1931 of 2231 steps (87%) done [Fri Nov 3 10:48:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-985.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-985.PRE.gff, analyses/output/Amil-MirMachine/Mir-985.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-985.PRE.unfiltered jobid: 1095 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-985.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-985.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-985.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1990.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1990.PRE.result jobid: 242 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1990.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1990.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:29 2023] Finished job 1095. 1932 of 2231 steps (87%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-985.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-985.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-985.PRE.filtered.gff jobid: 1662 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-985.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-985.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-985.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-985.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-985.PRE.filtered.fasta jobid: 2221 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-985.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-985.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-985.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:29 2023] Finished job 2221. 1933 of 2231 steps (87%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:29 2023] Finished job 1662. 1934 of 2231 steps (87%) done [Fri Nov 3 10:48:33 2023] Finished job 242. 1935 of 2231 steps (87%) done [Fri Nov 3 10:48:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1549.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1549.PRE.result jobid: 164 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1549.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1549.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1990.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1990.PRE.gff, analyses/output/Amil-MirMachine/Mir-1990.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1990.PRE.unfiltered jobid: 241 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1990.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1990.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1990.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:34 2023] Finished job 241. 1936 of 2231 steps (87%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1990.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1990.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1990.PRE.filtered.gff jobid: 1235 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1990.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1990.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1990.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1990.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1990.PRE.filtered.fasta jobid: 1794 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1990.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1990.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1990.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:34 2023] Finished job 1794. 1937 of 2231 steps (87%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:34 2023] Finished job 1235. 1938 of 2231 steps (87%) done [Fri Nov 3 10:48:39 2023] Finished job 164. 1939 of 2231 steps (87%) done [Fri Nov 3 10:48:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9701.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9701.PRE.result jobid: 1066 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9701.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9701.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1549.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1549.PRE.gff, analyses/output/Amil-MirMachine/Mir-1549.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1549.PRE.unfiltered jobid: 163 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1549.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-1549.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1549.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] Finished job 1036. 1940 of 2231 steps (87%) done Select jobs to execute... [Fri Nov 3 10:48:39 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3931.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3931.PRE.result jobid: 586 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3931.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3931.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-962.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-962.PRE.gff, analyses/output/Amil-MirMachine/Mir-962.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-962.PRE.unfiltered jobid: 1035 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-962.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-962.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-962.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] Finished job 163. 1941 of 2231 steps (87%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1549.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1549.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1549.PRE.filtered.gff jobid: 1196 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1549.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1549.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1549.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1549.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1549.PRE.filtered.fasta jobid: 1755 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1549.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1549.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1549.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] Finished job 1035. 1942 of 2231 steps (87%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-962.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:39 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-962.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-962.PRE.filtered.fasta jobid: 2191 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-962.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-962.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-962.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-962.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-962.PRE.filtered.gff jobid: 1632 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-962.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-962.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-962.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:39 2023] Finished job 1755. 1943 of 2231 steps (87%) done Select jobs to execute... [Fri Nov 3 10:48:39 2023] Finished job 2191. 1944 of 2231 steps (87%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:48:39 2023] Finished job 1196. 1945 of 2231 steps (87%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:39 2023] Finished job 1632. 1946 of 2231 steps (87%) done [Fri Nov 3 10:48:43 2023] Finished job 1066. 1947 of 2231 steps (87%) done [Fri Nov 3 10:48:43 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-196.PRE.CM output: analyses/output/Amil-MirMachine/Mir-196.PRE.result jobid: 224 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-196.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-196.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:43 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9701.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9701.PRE.gff, analyses/output/Amil-MirMachine/Mir-9701.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9701.PRE.unfiltered jobid: 1065 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9701.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9701.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9701.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:43 2023] Finished job 1065. 1948 of 2231 steps (87%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9701.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:43 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9701.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9701.PRE.filtered.fasta jobid: 2206 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9701.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9701.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9701.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:43 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9701.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9701.PRE.filtered.gff jobid: 1647 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9701.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9701.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9701.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:43 2023] Finished job 2206. 1949 of 2231 steps (87%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:43 2023] Finished job 1647. 1950 of 2231 steps (87%) done [Fri Nov 3 10:48:44 2023] Finished job 586. 1951 of 2231 steps (87%) done [Fri Nov 3 10:48:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3931.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3931.PRE.gff, analyses/output/Amil-MirMachine/Mir-3931.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3931.PRE.unfiltered jobid: 585 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3931.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3931.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3931.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-582.PRE.CM output: analyses/output/Amil-MirMachine/Mir-582.PRE.result jobid: 766 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-582.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-582.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:44 2023] Finished job 585. 1952 of 2231 steps (87%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3931.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3931.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3931.PRE.filtered.fasta jobid: 1966 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3931.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3931.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3931.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3931.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3931.PRE.filtered.gff jobid: 1407 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3931.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3931.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3931.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:45 2023] Finished job 1966. 1953 of 2231 steps (88%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:45 2023] Finished job 1407. 1954 of 2231 steps (88%) done [Fri Nov 3 10:48:50 2023] Finished job 224. 1955 of 2231 steps (88%) done [Fri Nov 3 10:48:50 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-320.PRE.CM output: analyses/output/Amil-MirMachine/Mir-320.PRE.result jobid: 514 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-320.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-320.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:50 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-196.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-196.PRE.gff, analyses/output/Amil-MirMachine/Mir-196.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-196.PRE.unfiltered jobid: 223 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-196.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-196.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-196.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:50 2023] Finished job 223. 1956 of 2231 steps (88%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-196.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:50 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-196.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-196.PRE.filtered.gff jobid: 1226 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-196.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-196.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-196.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:50 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-196.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-196.PRE.filtered.fasta jobid: 1785 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-196.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-196.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-196.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:50 2023] Finished job 1785. 1957 of 2231 steps (88%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:51 2023] Finished job 1226. 1958 of 2231 steps (88%) done [Fri Nov 3 10:48:51 2023] Finished job 766. 1959 of 2231 steps (88%) done [Fri Nov 3 10:48:51 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-582.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-582.PRE.gff, analyses/output/Amil-MirMachine/Mir-582.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-582.PRE.unfiltered jobid: 765 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-582.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-582.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-582.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:51 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1547.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1547.PRE.result jobid: 162 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1547.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1547.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:51 2023] Finished job 765. 1960 of 2231 steps (88%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-582.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:51 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-582.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-582.PRE.filtered.fasta jobid: 2056 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-582.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-582.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-582.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:51 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-582.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-582.PRE.filtered.gff jobid: 1497 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-582.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-582.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-582.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:51 2023] Finished job 2056. 1961 of 2231 steps (88%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:51 2023] Finished job 1497. 1962 of 2231 steps (88%) done [Fri Nov 3 10:48:56 2023] Finished job 162. 1963 of 2231 steps (88%) done [Fri Nov 3 10:48:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-122.PRE.CM output: analyses/output/Amil-MirMachine/Mir-122.PRE.result jobid: 46 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-122.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-122.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1547.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1547.PRE.gff, analyses/output/Amil-MirMachine/Mir-1547.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1547.PRE.unfiltered jobid: 161 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1547.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1547.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1547.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:56 2023] Finished job 161. 1964 of 2231 steps (88%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1547.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1547.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1547.PRE.filtered.fasta jobid: 1754 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1547.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1547.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1547.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1547.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1547.PRE.filtered.gff jobid: 1195 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1547.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1547.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1547.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:56 2023] Finished job 1754. 1965 of 2231 steps (88%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:57 2023] Finished job 1195. 1966 of 2231 steps (88%) done [Fri Nov 3 10:48:58 2023] Finished job 514. 1967 of 2231 steps (88%) done [Fri Nov 3 10:48:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-218.PRE.CM output: analyses/output/Amil-MirMachine/Mir-218.PRE.result jobid: 346 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-218.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-218.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:48:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-320.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-320.PRE.gff, analyses/output/Amil-MirMachine/Mir-320.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-320.PRE.unfiltered jobid: 513 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-320.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-320.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-320.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:58 2023] Finished job 513. 1968 of 2231 steps (88%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-320.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:48:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-320.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-320.PRE.filtered.gff jobid: 1371 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-320.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-320.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-320.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-320.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-320.PRE.filtered.fasta jobid: 1930 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-320.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-320.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-320.PRE resources: tmpdir=/tmp [Fri Nov 3 10:48:58 2023] Finished job 1930. 1969 of 2231 steps (88%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:48:58 2023] Finished job 1371. 1970 of 2231 steps (88%) done [Fri Nov 3 10:49:04 2023] Finished job 46. 1971 of 2231 steps (88%) done [Fri Nov 3 10:49:04 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-122.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-122.PRE.gff, analyses/output/Amil-MirMachine/Mir-122.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-122.PRE.unfiltered jobid: 45 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-122.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-122.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-122.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:04 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2012.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2012.PRE.result jobid: 282 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2012.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2012.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:04 2023] Finished job 45. 1972 of 2231 steps (88%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-122.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:04 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-122.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-122.PRE.filtered.fasta jobid: 1696 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-122.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-122.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-122.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:04 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-122.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-122.PRE.filtered.gff jobid: 1137 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-122.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-122.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-122.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:04 2023] Finished job 1696. 1973 of 2231 steps (88%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:04 2023] Finished job 1137. 1974 of 2231 steps (88%) done [Fri Nov 3 10:49:05 2023] Finished job 346. 1975 of 2231 steps (89%) done [Fri Nov 3 10:49:05 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-218.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-218.PRE.gff, analyses/output/Amil-MirMachine/Mir-218.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-218.PRE.unfiltered jobid: 345 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-218.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-218.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-218.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:05 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2970.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2970.PRE.result jobid: 462 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2970.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2970.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:05 2023] Finished job 345. 1976 of 2231 steps (89%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-218.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:05 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-218.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-218.PRE.filtered.fasta jobid: 1846 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-218.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-218.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-218.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:05 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-218.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-218.PRE.filtered.gff jobid: 1287 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-218.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-218.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-218.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:05 2023] Finished job 1846. 1977 of 2231 steps (89%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:05 2023] Finished job 1287. 1978 of 2231 steps (89%) done [Fri Nov 3 10:49:12 2023] Finished job 462. 1979 of 2231 steps (89%) done [Fri Nov 3 10:49:12 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2970.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2970.PRE.gff, analyses/output/Amil-MirMachine/Mir-2970.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2970.PRE.unfiltered jobid: 461 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2970.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2970.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2970.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:12 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-932.PRE.CM output: analyses/output/Amil-MirMachine/Mir-932.PRE.result jobid: 1002 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-932.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-932.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:12 2023] Finished job 461. 1980 of 2231 steps (89%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2970.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:12 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2970.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2970.PRE.filtered.gff jobid: 1345 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2970.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2970.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2970.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:12 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2970.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2970.PRE.filtered.fasta jobid: 1904 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2970.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2970.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2970.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:12 2023] Finished job 1904. 1981 of 2231 steps (89%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:12 2023] Finished job 1345. 1982 of 2231 steps (89%) done [Fri Nov 3 10:49:13 2023] Finished job 282. 1983 of 2231 steps (89%) done [Fri Nov 3 10:49:14 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-136.PRE.CM output: analyses/output/Amil-MirMachine/Mir-136.PRE.result jobid: 106 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-136.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-136.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:14 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2012.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2012.PRE.gff, analyses/output/Amil-MirMachine/Mir-2012.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2012.PRE.unfiltered jobid: 281 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2012.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2012.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2012.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:14 2023] Finished job 281. 1984 of 2231 steps (89%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2012.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2012.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2012.PRE.filtered.fasta jobid: 1814 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2012.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2012.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2012.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2012.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2012.PRE.filtered.gff jobid: 1255 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2012.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2012.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2012.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:14 2023] Finished job 1814. 1985 of 2231 steps (89%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:14 2023] Finished job 1255. 1986 of 2231 steps (89%) done [Fri Nov 3 10:49:19 2023] Finished job 1002. 1987 of 2231 steps (89%) done [Fri Nov 3 10:49:19 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-932.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-932.PRE.gff, analyses/output/Amil-MirMachine/Mir-932.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-932.PRE.unfiltered jobid: 1001 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-932.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-932.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-932.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1955.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1955.PRE.result jobid: 222 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1955.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1955.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] Finished job 1001. 1988 of 2231 steps (89%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-932.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:19 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-932.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-932.PRE.filtered.fasta jobid: 2174 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-932.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-932.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-932.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-932.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-932.PRE.filtered.gff jobid: 1615 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-932.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-932.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-932.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] Finished job 2174. 1989 of 2231 steps (89%) done Select jobs to execute... [Fri Nov 3 10:49:19 2023] Finished job 106. 1990 of 2231 steps (89%) done [Fri Nov 3 10:49:19 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-642.PRE.CM output: analyses/output/Amil-MirMachine/Mir-642.PRE.result jobid: 792 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-642.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-642.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-136.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-136.PRE.gff, analyses/output/Amil-MirMachine/Mir-136.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-136.PRE.unfiltered jobid: 105 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-136.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-136.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-136.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] Finished job 105. 1991 of 2231 steps (89%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-136.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:19 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-136.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-136.PRE.filtered.fasta jobid: 1726 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-136.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-136.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-136.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-136.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-136.PRE.filtered.gff jobid: 1167 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-136.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-136.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-136.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:19 2023] Finished job 1726. 1992 of 2231 steps (89%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:19 2023] Finished job 1615. 1993 of 2231 steps (89%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:19 2023] Finished job 1167. 1994 of 2231 steps (89%) done [Fri Nov 3 10:49:23 2023] Finished job 792. 1995 of 2231 steps (89%) done [Fri Nov 3 10:49:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-331.PRE.CM output: analyses/output/Amil-MirMachine/Mir-331.PRE.result jobid: 530 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-331.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-331.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-642.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-642.PRE.gff, analyses/output/Amil-MirMachine/Mir-642.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-642.PRE.unfiltered jobid: 791 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-642.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-642.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-642.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:23 2023] Finished job 791. 1996 of 2231 steps (89%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-642.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-642.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-642.PRE.filtered.gff jobid: 1510 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-642.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-642.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-642.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-642.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-642.PRE.filtered.fasta jobid: 2069 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-642.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-642.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-642.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:23 2023] Finished job 2069. 1997 of 2231 steps (90%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:23 2023] Finished job 1510. 1998 of 2231 steps (90%) done [Fri Nov 3 10:49:24 2023] Finished job 222. 1999 of 2231 steps (90%) done [Fri Nov 3 10:49:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1955.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1955.PRE.gff, analyses/output/Amil-MirMachine/Mir-1955.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1955.PRE.unfiltered jobid: 221 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1955.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1955.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1955.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2018.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2018.PRE.result jobid: 290 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2018.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2018.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:24 2023] Finished job 221. 2000 of 2231 steps (90%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1955.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1955.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1955.PRE.filtered.gff jobid: 1225 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1955.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1955.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1955.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1955.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1955.PRE.filtered.fasta jobid: 1784 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1955.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1955.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1955.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:24 2023] Finished job 1784. 2001 of 2231 steps (90%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:24 2023] Finished job 1225. 2002 of 2231 steps (90%) done [Fri Nov 3 10:49:25 2023] Finished job 530. 2003 of 2231 steps (90%) done [Fri Nov 3 10:49:25 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-486.PRE.CM output: analyses/output/Amil-MirMachine/Mir-486.PRE.result jobid: 672 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-486.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-486.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:25 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-331.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-331.PRE.gff, analyses/output/Amil-MirMachine/Mir-331.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-331.PRE.unfiltered jobid: 529 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-331.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-331.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-331.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:25 2023] Finished job 529. 2004 of 2231 steps (90%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-331.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:26 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-331.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-331.PRE.filtered.gff jobid: 1379 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-331.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-331.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-331.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:26 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-331.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-331.PRE.filtered.fasta jobid: 1938 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-331.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-331.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-331.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:26 2023] Finished job 1938. 2005 of 2231 steps (90%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:26 2023] Finished job 1379. 2006 of 2231 steps (90%) done [Fri Nov 3 10:49:29 2023] Finished job 672. 2007 of 2231 steps (90%) done [Fri Nov 3 10:49:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9699.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9699.PRE.result jobid: 1062 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9699.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9699.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-486.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-486.PRE.gff, analyses/output/Amil-MirMachine/Mir-486.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-486.PRE.unfiltered jobid: 671 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-486.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-486.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-486.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:29 2023] Finished job 671. 2008 of 2231 steps (90%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-486.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-486.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-486.PRE.filtered.gff jobid: 1450 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-486.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-486.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-486.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-486.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-486.PRE.filtered.fasta jobid: 2009 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-486.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-486.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-486.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:29 2023] Finished job 2009. 2009 of 2231 steps (90%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:30 2023] Finished job 1450. 2010 of 2231 steps (90%) done [Fri Nov 3 10:49:32 2023] Finished job 290. 2011 of 2231 steps (90%) done [Fri Nov 3 10:49:33 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2722.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2722.PRE.result jobid: 432 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2722.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2722.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:33 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2018.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2018.PRE.gff, analyses/output/Amil-MirMachine/Mir-2018.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2018.PRE.unfiltered jobid: 289 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2018.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-2018.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2018.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:33 2023] Finished job 289. 2012 of 2231 steps (90%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2018.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2018.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2018.PRE.filtered.gff jobid: 1259 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2018.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2018.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2018.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2018.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2018.PRE.filtered.fasta jobid: 1818 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2018.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2018.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2018.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:33 2023] Finished job 1818. 2013 of 2231 steps (90%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:33 2023] Finished job 1259. 2014 of 2231 steps (90%) done [Fri Nov 3 10:49:34 2023] Finished job 1062. 2015 of 2231 steps (90%) done [Fri Nov 3 10:49:34 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-983.PRE.CM output: analyses/output/Amil-MirMachine/Mir-983.PRE.result jobid: 1092 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-983.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-983.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:34 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9699.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9699.PRE.gff, analyses/output/Amil-MirMachine/Mir-9699.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9699.PRE.unfiltered jobid: 1061 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9699.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9699.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9699.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:34 2023] Finished job 1061. 2016 of 2231 steps (90%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9699.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:34 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9699.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9699.PRE.filtered.gff jobid: 1645 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9699.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9699.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9699.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:34 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9699.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9699.PRE.filtered.fasta jobid: 2204 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9699.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9699.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9699.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:34 2023] Finished job 2204. 2017 of 2231 steps (90%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:35 2023] Finished job 1645. 2018 of 2231 steps (90%) done [Fri Nov 3 10:49:37 2023] Finished job 432. 2019 of 2231 steps (90%) done [Fri Nov 3 10:49:37 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-351.PRE.CM output: analyses/output/Amil-MirMachine/Mir-351.PRE.result jobid: 552 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-351.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-351.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:37 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2722.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2722.PRE.gff, analyses/output/Amil-MirMachine/Mir-2722.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2722.PRE.unfiltered jobid: 431 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2722.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2722.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2722.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:37 2023] Finished job 431. 2020 of 2231 steps (91%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2722.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:37 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2722.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2722.PRE.filtered.gff jobid: 1330 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2722.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2722.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2722.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:37 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2722.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2722.PRE.filtered.fasta jobid: 1889 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2722.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2722.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2722.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:37 2023] Finished job 1889. 2021 of 2231 steps (91%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:37 2023] Finished job 1330. 2022 of 2231 steps (91%) done [Fri Nov 3 10:49:46 2023] Finished job 1092. 2023 of 2231 steps (91%) done [Fri Nov 3 10:49:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-983.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-983.PRE.gff, analyses/output/Amil-MirMachine/Mir-983.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-983.PRE.unfiltered jobid: 1091 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-983.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-983.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-983.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-961.PRE.CM output: analyses/output/Amil-MirMachine/Mir-961.PRE.result jobid: 1032 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-961.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-961.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:46 2023] Finished job 1091. 2024 of 2231 steps (91%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-983.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-983.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-983.PRE.filtered.fasta jobid: 2219 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-983.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-983.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-983.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-983.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-983.PRE.filtered.gff jobid: 1660 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-983.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-983.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-983.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:46 2023] Finished job 2219. 2025 of 2231 steps (91%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:47 2023] Finished job 1660. 2026 of 2231 steps (91%) done [Fri Nov 3 10:49:49 2023] Finished job 552. 2027 of 2231 steps (91%) done [Fri Nov 3 10:49:49 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2690.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2690.PRE.result jobid: 420 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2690.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2690.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:49 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-351.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-351.PRE.gff, analyses/output/Amil-MirMachine/Mir-351.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-351.PRE.unfiltered jobid: 551 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-351.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-351.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-351.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:49 2023] Finished job 551. 2028 of 2231 steps (91%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-351.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:49 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-351.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-351.PRE.filtered.gff jobid: 1390 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-351.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-351.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-351.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:49 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-351.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-351.PRE.filtered.fasta jobid: 1949 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-351.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-351.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-351.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:49 2023] Finished job 1949. 2029 of 2231 steps (91%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:49 2023] Finished job 1390. 2030 of 2231 steps (91%) done [Fri Nov 3 10:49:58 2023] Finished job 1032. 2031 of 2231 steps (91%) done [Fri Nov 3 10:49:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-961.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-961.PRE.gff, analyses/output/Amil-MirMachine/Mir-961.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-961.PRE.unfiltered jobid: 1031 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-961.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-961.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-961.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-9619.PRE.CM output: analyses/output/Amil-MirMachine/Mir-9619.PRE.result jobid: 1034 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9619.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-9619.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] Finished job 1031. 2032 of 2231 steps (91%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-961.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-961.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-961.PRE.filtered.gff jobid: 1630 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-961.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-961.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-961.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-961.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-961.PRE.filtered.fasta jobid: 2189 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-961.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-961.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-961.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] Finished job 2189. 2033 of 2231 steps (91%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:58 2023] Finished job 1630. 2034 of 2231 steps (91%) done [Fri Nov 3 10:49:58 2023] Finished job 420. 2035 of 2231 steps (91%) done [Fri Nov 3 10:49:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3200.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3200.PRE.result jobid: 516 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3200.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3200.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2690.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2690.PRE.gff, analyses/output/Amil-MirMachine/Mir-2690.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2690.PRE.unfiltered jobid: 419 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2690.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2690.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2690.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] Finished job 419. 2036 of 2231 steps (91%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2690.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:49:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2690.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2690.PRE.filtered.fasta jobid: 1883 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2690.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2690.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2690.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2690.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2690.PRE.filtered.gff jobid: 1324 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2690.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2690.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2690.PRE resources: tmpdir=/tmp [Fri Nov 3 10:49:58 2023] Finished job 1883. 2037 of 2231 steps (91%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:49:59 2023] Finished job 1324. 2038 of 2231 steps (91%) done [Fri Nov 3 10:50:02 2023] Finished job 516. 2039 of 2231 steps (91%) done [Fri Nov 3 10:50:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-376.PRE.CM output: analyses/output/Amil-MirMachine/Mir-376.PRE.result jobid: 576 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-376.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-376.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3200.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3200.PRE.gff, analyses/output/Amil-MirMachine/Mir-3200.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3200.PRE.unfiltered jobid: 515 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3200.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3200.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3200.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] Finished job 1034. 2040 of 2231 steps (91%) done Select jobs to execute... [Fri Nov 3 10:50:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2009.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2009.PRE.result jobid: 276 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2009.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2009.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-9619.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-9619.PRE.gff, analyses/output/Amil-MirMachine/Mir-9619.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-9619.PRE.unfiltered jobid: 1033 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9619.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9619.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-9619.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] Finished job 515. 2041 of 2231 steps (91%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3200.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3200.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3200.PRE.filtered.fasta jobid: 1931 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3200.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3200.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3200.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3200.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3200.PRE.filtered.gff jobid: 1372 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3200.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3200.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3200.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] Finished job 1033. 2042 of 2231 steps (92%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-9619.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-9619.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9619.PRE.filtered.gff jobid: 1631 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9619.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9619.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9619.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-9619.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-9619.PRE.filtered.fasta jobid: 2190 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-9619.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-9619.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-9619.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:02 2023] Finished job 1931. 2043 of 2231 steps (92%) done Select jobs to execute... [Fri Nov 3 10:50:02 2023] Finished job 2190. 2044 of 2231 steps (92%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:02 2023] Finished job 1372. 2045 of 2231 steps (92%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:02 2023] Finished job 1631. 2046 of 2231 steps (92%) done [Fri Nov 3 10:50:09 2023] Finished job 576. 2047 of 2231 steps (92%) done [Fri Nov 3 10:50:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4874.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4874.PRE.result jobid: 696 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4874.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4874.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-376.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-376.PRE.gff, analyses/output/Amil-MirMachine/Mir-376.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-376.PRE.unfiltered jobid: 575 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-376.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-376.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-376.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:09 2023] Finished job 575. 2048 of 2231 steps (92%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-376.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:09 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-376.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-376.PRE.filtered.fasta jobid: 1961 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-376.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-376.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-376.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:09 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-376.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-376.PRE.filtered.gff jobid: 1402 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-376.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-376.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-376.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:09 2023] Finished job 1961. 2049 of 2231 steps (92%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:09 2023] Finished job 1402. 2050 of 2231 steps (92%) done [Fri Nov 3 10:50:12 2023] Finished job 696. 2051 of 2231 steps (92%) done [Fri Nov 3 10:50:12 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1996.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1996.PRE.result jobid: 252 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1996.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1996.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:12 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4874.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4874.PRE.gff, analyses/output/Amil-MirMachine/Mir-4874.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4874.PRE.unfiltered jobid: 695 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4874.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4874.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4874.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:12 2023] Finished job 695. 2052 of 2231 steps (92%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4874.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:12 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4874.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4874.PRE.filtered.fasta jobid: 2021 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4874.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4874.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4874.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:12 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4874.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4874.PRE.filtered.gff jobid: 1462 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4874.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4874.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4874.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:13 2023] Finished job 2021. 2053 of 2231 steps (92%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:13 2023] Finished job 1462. 2054 of 2231 steps (92%) done [Fri Nov 3 10:50:13 2023] Finished job 276. 2055 of 2231 steps (92%) done [Fri Nov 3 10:50:13 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-92.PRE.CM output: analyses/output/Amil-MirMachine/Mir-92.PRE.result jobid: 996 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-92.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-92.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:13 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2009.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2009.PRE.gff, analyses/output/Amil-MirMachine/Mir-2009.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2009.PRE.unfiltered jobid: 275 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2009.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2009.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2009.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:13 2023] Finished job 275. 2056 of 2231 steps (92%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2009.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:13 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2009.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2009.PRE.filtered.fasta jobid: 1811 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2009.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2009.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2009.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:13 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2009.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2009.PRE.filtered.gff jobid: 1252 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2009.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2009.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2009.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:13 2023] Finished job 1811. 2057 of 2231 steps (92%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:14 2023] Finished job 1252. 2058 of 2231 steps (92%) done [Fri Nov 3 10:50:17 2023] Finished job 252. 2059 of 2231 steps (92%) done [Fri Nov 3 10:50:17 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-31.PRE.CM output: analyses/output/Amil-MirMachine/Mir-31.PRE.result jobid: 492 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-31.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-31.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:17 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1996.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1996.PRE.gff, analyses/output/Amil-MirMachine/Mir-1996.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1996.PRE.unfiltered jobid: 251 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1996.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1996.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1996.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:17 2023] Finished job 251. 2060 of 2231 steps (92%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1996.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:17 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1996.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1996.PRE.filtered.fasta jobid: 1799 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1996.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1996.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1996.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:17 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1996.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1996.PRE.filtered.gff jobid: 1240 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1996.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1996.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1996.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:17 2023] Finished job 1799. 2061 of 2231 steps (92%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:17 2023] Finished job 1240. 2062 of 2231 steps (92%) done [Fri Nov 3 10:50:23 2023] Finished job 996. 2063 of 2231 steps (92%) done [Fri Nov 3 10:50:23 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-744.PRE.CM output: analyses/output/Amil-MirMachine/Mir-744.PRE.result jobid: 936 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-744.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-744.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:23 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-92.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-92.PRE.gff, analyses/output/Amil-MirMachine/Mir-92.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-92.PRE.unfiltered jobid: 995 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-92.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-92.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-92.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:23 2023] Finished job 995. 2064 of 2231 steps (93%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-92.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:23 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-92.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-92.PRE.filtered.fasta jobid: 2171 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-92.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-92.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-92.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:23 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-92.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-92.PRE.filtered.gff jobid: 1612 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-92.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-92.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-92.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:23 2023] Finished job 2171. 2065 of 2231 steps (93%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:50:24 2023] Finished job 492. 2066 of 2231 steps (93%) done ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:24 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1343.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1343.PRE.result jobid: 102 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1343.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1343.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:24 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-31.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-31.PRE.gff, analyses/output/Amil-MirMachine/Mir-31.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-31.PRE.unfiltered jobid: 491 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-31.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-31.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-31.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:24 2023] Finished job 1612. 2067 of 2231 steps (93%) done Select jobs to execute... [Fri Nov 3 10:50:24 2023] Finished job 491. 2068 of 2231 steps (93%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-31.PRE.ext.gff. [Fri Nov 3 10:50:24 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-31.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-31.PRE.filtered.fasta jobid: 1919 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-31.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-31.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-31.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:24 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-31.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-31.PRE.filtered.gff jobid: 1360 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-31.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-31.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-31.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:24 2023] Finished job 1919. 2069 of 2231 steps (93%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:24 2023] Finished job 1360. 2070 of 2231 steps (93%) done [Fri Nov 3 10:50:26 2023] Finished job 102. 2071 of 2231 steps (93%) done [Fri Nov 3 10:50:26 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4820.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4820.PRE.result jobid: 644 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4820.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4820.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:26 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1343.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1343.PRE.gff, analyses/output/Amil-MirMachine/Mir-1343.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1343.PRE.unfiltered jobid: 101 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1343.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1343.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1343.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:27 2023] Finished job 101. 2072 of 2231 steps (93%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1343.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1343.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1343.PRE.filtered.gff jobid: 1165 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1343.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1343.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1343.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1343.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1343.PRE.filtered.fasta jobid: 1724 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1343.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1343.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1343.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:27 2023] Finished job 936. 2073 of 2231 steps (93%) done Select jobs to execute... [Fri Nov 3 10:50:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-76.PRE.CM output: analyses/output/Amil-MirMachine/Mir-76.PRE.result jobid: 942 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-76.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-76.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-744.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-744.PRE.gff, analyses/output/Amil-MirMachine/Mir-744.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-744.PRE.unfiltered jobid: 935 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-744.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-744.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-744.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:27 2023] Finished job 1724. 2074 of 2231 steps (93%) done Select jobs to execute... [Fri Nov 3 10:50:27 2023] Finished job 935. 2075 of 2231 steps (93%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-744.PRE.ext.gff. [Fri Nov 3 10:50:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-744.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-744.PRE.filtered.fasta jobid: 2141 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-744.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-744.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-744.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-744.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-744.PRE.filtered.gff jobid: 1582 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-744.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-744.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-744.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:27 2023] Finished job 2141. 2076 of 2231 steps (93%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:27 2023] Finished job 1165. 2077 of 2231 steps (93%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:27 2023] Finished job 1582. 2078 of 2231 steps (93%) done [Fri Nov 3 10:50:31 2023] Finished job 644. 2079 of 2231 steps (93%) done [Fri Nov 3 10:50:31 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7304.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7304.PRE.result jobid: 884 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7304.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7304.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:31 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4820.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4820.PRE.gff, analyses/output/Amil-MirMachine/Mir-4820.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4820.PRE.unfiltered jobid: 643 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4820.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4820.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4820.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:31 2023] Finished job 643. 2080 of 2231 steps (93%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4820.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:31 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4820.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4820.PRE.filtered.gff jobid: 1436 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4820.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4820.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4820.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:31 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4820.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4820.PRE.filtered.fasta jobid: 1995 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4820.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4820.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4820.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:31 2023] Finished job 1995. 2081 of 2231 steps (93%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:31 2023] Finished job 1436. 2082 of 2231 steps (93%) done [Fri Nov 3 10:50:35 2023] Finished job 942. 2083 of 2231 steps (93%) done [Fri Nov 3 10:50:35 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-7.PRE.CM output: analyses/output/Amil-MirMachine/Mir-7.PRE.result jobid: 824 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-7.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-76.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-76.PRE.gff, analyses/output/Amil-MirMachine/Mir-76.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-76.PRE.unfiltered jobid: 941 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-76.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-76.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-76.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] Finished job 941. 2084 of 2231 steps (93%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-76.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-76.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-76.PRE.filtered.gff jobid: 1585 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-76.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-76.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-76.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-76.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-76.PRE.filtered.fasta jobid: 2144 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-76.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-76.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-76.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] Finished job 2144. 2085 of 2231 steps (93%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:35 2023] Finished job 1585. 2086 of 2231 steps (94%) done [Fri Nov 3 10:50:35 2023] Finished job 884. 2087 of 2231 steps (94%) done [Fri Nov 3 10:50:35 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-217.PRE.CM output: analyses/output/Amil-MirMachine/Mir-217.PRE.result jobid: 344 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-217.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-217.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7304.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7304.PRE.gff, analyses/output/Amil-MirMachine/Mir-7304.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7304.PRE.unfiltered jobid: 883 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7304.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7304.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7304.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] Finished job 883. 2088 of 2231 steps (94%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7304.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:35 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7304.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7304.PRE.filtered.gff jobid: 1556 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7304.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7304.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7304.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7304.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7304.PRE.filtered.fasta jobid: 2115 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7304.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7304.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7304.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:35 2023] Finished job 2115. 2089 of 2231 steps (94%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:36 2023] Finished job 1556. 2090 of 2231 steps (94%) done [Fri Nov 3 10:50:44 2023] Finished job 344. 2091 of 2231 steps (94%) done [Fri Nov 3 10:50:44 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-970.PRE.CM output: analyses/output/Amil-MirMachine/Mir-970.PRE.result jobid: 1064 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-970.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-970.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:44 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-217.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-217.PRE.gff, analyses/output/Amil-MirMachine/Mir-217.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-217.PRE.unfiltered jobid: 343 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-217.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-217.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-217.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:44 2023] Finished job 343. 2092 of 2231 steps (94%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-217.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:44 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-217.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-217.PRE.filtered.gff jobid: 1286 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-217.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-217.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-217.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:44 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-217.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-217.PRE.filtered.fasta jobid: 1845 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-217.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-217.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-217.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:44 2023] Finished job 1845. 2093 of 2231 steps (94%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:44 2023] Finished job 1286. 2094 of 2231 steps (94%) done [Fri Nov 3 10:50:52 2023] Finished job 1064. 2095 of 2231 steps (94%) done [Fri Nov 3 10:50:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-970.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-970.PRE.gff, analyses/output/Amil-MirMachine/Mir-970.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-970.PRE.unfiltered jobid: 1063 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-970.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-970.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-970.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2006.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2006.PRE.result jobid: 270 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2006.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2006.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:52 2023] Finished job 1063. 2096 of 2231 steps (94%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-970.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-970.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-970.PRE.filtered.gff jobid: 1646 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-970.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-970.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-970.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-970.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-970.PRE.filtered.fasta jobid: 2205 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-970.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-970.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-970.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:52 2023] Finished job 2205. 2097 of 2231 steps (94%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:52 2023] Finished job 1646. 2098 of 2231 steps (94%) done [Fri Nov 3 10:50:52 2023] Finished job 824. 2099 of 2231 steps (94%) done [Fri Nov 3 10:50:52 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3173.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3173.PRE.result jobid: 510 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3173.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3173.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:52 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-7.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-7.PRE.gff, analyses/output/Amil-MirMachine/Mir-7.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-7.PRE.unfiltered jobid: 823 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-7.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:52 2023] Finished job 823. 2100 of 2231 steps (94%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-7.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:52 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-7.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7.PRE.filtered.gff jobid: 1526 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:52 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-7.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-7.PRE.filtered.fasta jobid: 2085 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-7.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-7.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-7.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:53 2023] Finished job 2085. 2101 of 2231 steps (94%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:53 2023] Finished job 1526. 2102 of 2231 steps (94%) done [Fri Nov 3 10:50:56 2023] Finished job 270. 2103 of 2231 steps (94%) done [Fri Nov 3 10:50:56 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2006.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2006.PRE.gff, analyses/output/Amil-MirMachine/Mir-2006.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2006.PRE.unfiltered jobid: 269 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2006.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-2006.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2006.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:56 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4871.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4871.PRE.result jobid: 690 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4871.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4871.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:56 2023] Finished job 269. 2104 of 2231 steps (94%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2006.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:56 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2006.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2006.PRE.filtered.gff jobid: 1249 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2006.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2006.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2006.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:56 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2006.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2006.PRE.filtered.fasta jobid: 1808 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2006.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2006.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2006.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:56 2023] Finished job 1808. 2105 of 2231 steps (94%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:56 2023] Finished job 1249. 2106 of 2231 steps (94%) done [Fri Nov 3 10:50:59 2023] Finished job 510. 2107 of 2231 steps (94%) done [Fri Nov 3 10:50:59 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3173.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3173.PRE.gff, analyses/output/Amil-MirMachine/Mir-3173.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3173.PRE.unfiltered jobid: 509 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3173.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3173.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3173.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:59 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-671.PRE.CM output: analyses/output/Amil-MirMachine/Mir-671.PRE.result jobid: 810 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-671.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-671.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:50:59 2023] Finished job 509. 2108 of 2231 steps (94%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3173.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:50:59 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3173.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3173.PRE.filtered.gff jobid: 1369 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3173.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3173.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3173.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:59 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3173.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3173.PRE.filtered.fasta jobid: 1928 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3173.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3173.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3173.PRE resources: tmpdir=/tmp [Fri Nov 3 10:50:59 2023] Finished job 1928. 2109 of 2231 steps (95%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:50:59 2023] Finished job 1369. 2110 of 2231 steps (95%) done [Fri Nov 3 10:51:00 2023] Finished job 690. 2111 of 2231 steps (95%) done [Fri Nov 3 10:51:00 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4871.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4871.PRE.gff, analyses/output/Amil-MirMachine/Mir-4871.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4871.PRE.unfiltered jobid: 689 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4871.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4871.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4871.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:00 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-984.PRE.CM output: analyses/output/Amil-MirMachine/Mir-984.PRE.result jobid: 1094 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-984.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-984.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:00 2023] Finished job 689. 2112 of 2231 steps (95%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4871.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:00 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4871.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4871.PRE.filtered.gff jobid: 1459 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4871.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4871.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4871.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:00 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4871.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4871.PRE.filtered.fasta jobid: 2018 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4871.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4871.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4871.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:00 2023] Finished job 2018. 2113 of 2231 steps (95%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:00 2023] Finished job 1459. 2114 of 2231 steps (95%) done [Fri Nov 3 10:51:02 2023] Finished job 810. 2115 of 2231 steps (95%) done [Fri Nov 3 10:51:02 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-671.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-671.PRE.gff, analyses/output/Amil-MirMachine/Mir-671.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-671.PRE.unfiltered jobid: 809 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-671.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-671.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-671.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:02 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1542.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1542.PRE.result jobid: 158 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1542.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1542.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:02 2023] Finished job 809. 2116 of 2231 steps (95%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-671.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:02 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-671.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-671.PRE.filtered.gff jobid: 1519 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-671.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-671.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-671.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:02 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-671.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-671.PRE.filtered.fasta jobid: 2078 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-671.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-671.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-671.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:02 2023] Finished job 2078. 2117 of 2231 steps (95%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:03 2023] Finished job 1519. 2118 of 2231 steps (95%) done [Fri Nov 3 10:51:05 2023] Finished job 1094. 2119 of 2231 steps (95%) done [Fri Nov 3 10:51:05 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-193.PRE.CM output: analyses/output/Amil-MirMachine/Mir-193.PRE.result jobid: 218 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-193.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-193.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:05 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-984.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-984.PRE.gff, analyses/output/Amil-MirMachine/Mir-984.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-984.PRE.unfiltered jobid: 1093 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-984.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-984.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:06 2023] Finished job 1093. 2120 of 2231 steps (95%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-984.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-984.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-984.PRE.filtered.gff jobid: 1661 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-984.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-984.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-984.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-984.PRE.filtered.fasta jobid: 2220 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-984.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-984.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-984.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:06 2023] Finished job 2220. 2121 of 2231 steps (95%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:06 2023] Finished job 1661. 2122 of 2231 steps (95%) done [Fri Nov 3 10:51:07 2023] Finished job 158. 2123 of 2231 steps (95%) done [Fri Nov 3 10:51:07 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1542.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1542.PRE.gff, analyses/output/Amil-MirMachine/Mir-1542.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1542.PRE.unfiltered jobid: 157 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1542.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1542.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:07 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-378.PRE.CM output: analyses/output/Amil-MirMachine/Mir-378.PRE.result jobid: 578 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-378.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-378.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:07 2023] Finished job 157. 2124 of 2231 steps (95%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1542.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:07 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1542.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1542.PRE.filtered.fasta jobid: 1752 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1542.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1542.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:07 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1542.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1542.PRE.filtered.gff jobid: 1193 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1542.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1542.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1542.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:07 2023] Finished job 1752. 2125 of 2231 steps (95%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:08 2023] Finished job 1193. 2126 of 2231 steps (95%) done [Fri Nov 3 10:51:10 2023] Finished job 218. 2127 of 2231 steps (95%) done [Fri Nov 3 10:51:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-193.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-193.PRE.gff, analyses/output/Amil-MirMachine/Mir-193.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-193.PRE.unfiltered jobid: 217 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-193.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-193.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-193.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2954.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2954.PRE.result jobid: 458 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2954.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2954.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:10 2023] Finished job 217. 2128 of 2231 steps (95%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-193.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:11 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-193.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-193.PRE.filtered.fasta jobid: 1782 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-193.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-193.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-193.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:11 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-193.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-193.PRE.filtered.gff jobid: 1223 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-193.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-193.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-193.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:11 2023] Finished job 1782. 2129 of 2231 steps (95%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:11 2023] Finished job 1223. 2130 of 2231 steps (95%) done [Fri Nov 3 10:51:12 2023] Finished job 578. 2131 of 2231 steps (96%) done [Fri Nov 3 10:51:12 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-378.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-378.PRE.gff, analyses/output/Amil-MirMachine/Mir-378.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-378.PRE.unfiltered jobid: 577 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-378.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-378.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-378.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:12 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-674.PRE.CM output: analyses/output/Amil-MirMachine/Mir-674.PRE.result jobid: 818 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-674.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-674.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:12 2023] Finished job 577. 2132 of 2231 steps (96%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-378.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:12 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-378.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-378.PRE.filtered.fasta jobid: 1962 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-378.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-378.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-378.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:12 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-378.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-378.PRE.filtered.gff jobid: 1403 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-378.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-378.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-378.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:12 2023] Finished job 1962. 2133 of 2231 steps (96%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:12 2023] Finished job 1403. 2134 of 2231 steps (96%) done [Fri Nov 3 10:51:14 2023] Finished job 458. 2135 of 2231 steps (96%) done [Fri Nov 3 10:51:14 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2954.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2954.PRE.gff, analyses/output/Amil-MirMachine/Mir-2954.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2954.PRE.unfiltered jobid: 457 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2954.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-2954.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2954.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:14 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2583.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2583.PRE.result jobid: 406 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2583.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2583.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:14 2023] Finished job 457. 2136 of 2231 steps (96%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2954.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:14 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2954.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2954.PRE.filtered.fasta jobid: 1902 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2954.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2954.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2954.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:14 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2954.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2954.PRE.filtered.gff jobid: 1343 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2954.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2954.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2954.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:14 2023] Finished job 1902. 2137 of 2231 steps (96%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:15 2023] Finished job 1343. 2138 of 2231 steps (96%) done [Fri Nov 3 10:51:15 2023] Finished job 818. 2139 of 2231 steps (96%) done [Fri Nov 3 10:51:15 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-674.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-674.PRE.gff, analyses/output/Amil-MirMachine/Mir-674.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-674.PRE.unfiltered jobid: 817 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-674.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-674.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-674.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:15 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-33.PRE.CM output: analyses/output/Amil-MirMachine/Mir-33.PRE.result jobid: 526 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-33.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-33.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:15 2023] Finished job 817. 2140 of 2231 steps (96%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-674.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:15 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-674.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-674.PRE.filtered.fasta jobid: 2082 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-674.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-674.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-674.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:15 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-674.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-674.PRE.filtered.gff jobid: 1523 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-674.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-674.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-674.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:15 2023] Finished job 2082. 2141 of 2231 steps (96%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:15 2023] Finished job 1523. 2142 of 2231 steps (96%) done [Fri Nov 3 10:51:18 2023] Finished job 406. 2143 of 2231 steps (96%) done [Fri Nov 3 10:51:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3072.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3072.PRE.result jobid: 484 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3072.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3072.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2583.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2583.PRE.gff, analyses/output/Amil-MirMachine/Mir-2583.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2583.PRE.unfiltered jobid: 405 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2583.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-2583.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2583.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:18 2023] Finished job 405. 2144 of 2231 steps (96%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2583.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:18 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2583.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2583.PRE.filtered.fasta jobid: 1876 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2583.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2583.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2583.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:18 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2583.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2583.PRE.filtered.gff jobid: 1317 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2583.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2583.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2583.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:18 2023] Finished job 1876. 2145 of 2231 steps (96%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:18 2023] Finished job 1317. 2146 of 2231 steps (96%) done [Fri Nov 3 10:51:21 2023] Finished job 484. 2147 of 2231 steps (96%) done [Fri Nov 3 10:51:21 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-2015.PRE.CM output: analyses/output/Amil-MirMachine/Mir-2015.PRE.result jobid: 286 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2015.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-2015.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:21 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3072.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3072.PRE.gff, analyses/output/Amil-MirMachine/Mir-3072.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3072.PRE.unfiltered jobid: 483 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3072.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3072.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3072.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:21 2023] Finished job 483. 2148 of 2231 steps (96%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3072.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:21 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3072.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3072.PRE.filtered.fasta jobid: 1915 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3072.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3072.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3072.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:21 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3072.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3072.PRE.filtered.gff jobid: 1356 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3072.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3072.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3072.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:21 2023] Finished job 1915. 2149 of 2231 steps (96%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:21 2023] Finished job 1356. 2150 of 2231 steps (96%) done [Fri Nov 3 10:51:29 2023] Finished job 526. 2151 of 2231 steps (96%) done [Fri Nov 3 10:51:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-33.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-33.PRE.gff, analyses/output/Amil-MirMachine/Mir-33.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-33.PRE.unfiltered jobid: 525 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-33.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-33.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-33.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-275.PRE.CM output: analyses/output/Amil-MirMachine/Mir-275.PRE.result jobid: 434 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-275.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-275.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:29 2023] Finished job 525. 2152 of 2231 steps (96%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-33.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:29 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-33.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-33.PRE.filtered.fasta jobid: 1936 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-33.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-33.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-33.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:29 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-33.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-33.PRE.filtered.gff jobid: 1377 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-33.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-33.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-33.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:29 2023] Finished job 1936. 2153 of 2231 steps (97%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:29 2023] Finished job 286. 2154 of 2231 steps (97%) done [Fri Nov 3 10:51:29 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-2015.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-2015.PRE.gff, analyses/output/Amil-MirMachine/Mir-2015.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-2015.PRE.unfiltered jobid: 285 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2015.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2015.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-2015.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:29 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4860.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4860.PRE.result jobid: 674 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4860.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4860.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:29 2023] Finished job 1377. 2155 of 2231 steps (97%) done Select jobs to execute... [Fri Nov 3 10:51:30 2023] Finished job 285. 2156 of 2231 steps (97%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-2015.PRE.ext.gff. [Fri Nov 3 10:51:30 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-2015.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2015.PRE.filtered.fasta jobid: 1816 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2015.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2015.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2015.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:30 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-2015.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-2015.PRE.filtered.gff jobid: 1257 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-2015.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-2015.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-2015.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:30 2023] Finished job 1816. 2157 of 2231 steps (97%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:30 2023] Finished job 1257. 2158 of 2231 steps (97%) done [Fri Nov 3 10:51:33 2023] Finished job 434. 2159 of 2231 steps (97%) done [Fri Nov 3 10:51:33 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-275.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-275.PRE.gff, analyses/output/Amil-MirMachine/Mir-275.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-275.PRE.unfiltered jobid: 433 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-275.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-275.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-275.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:33 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1998.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1998.PRE.result jobid: 256 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1998.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1998.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:33 2023] Finished job 433. 2160 of 2231 steps (97%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-275.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-275.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-275.PRE.filtered.gff jobid: 1331 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-275.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-275.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-275.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-275.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-275.PRE.filtered.fasta jobid: 1890 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-275.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-275.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-275.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:33 2023] Finished job 1890. 2161 of 2231 steps (97%) done Select jobs to execute... [Fri Nov 3 10:51:33 2023] Finished job 674. 2162 of 2231 steps (97%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:51:33 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4860.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4860.PRE.gff, analyses/output/Amil-MirMachine/Mir-4860.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4860.PRE.unfiltered jobid: 673 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4860.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4860.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-4860.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:33 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-357.PRE.CM output: analyses/output/Amil-MirMachine/Mir-357.PRE.result jobid: 556 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-357.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-357.PRE threads: 15 resources: tmpdir=/tmp ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:33 2023] Finished job 673. 2163 of 2231 steps (97%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4860.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4860.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4860.PRE.filtered.gff jobid: 1451 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4860.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4860.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4860.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4860.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4860.PRE.filtered.fasta jobid: 2010 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4860.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4860.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4860.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:33 2023] Finished job 1331. 2164 of 2231 steps (97%) done Select jobs to execute... [Fri Nov 3 10:51:33 2023] Finished job 2010. 2165 of 2231 steps (97%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:34 2023] Finished job 1451. 2166 of 2231 steps (97%) done [Fri Nov 3 10:51:40 2023] Finished job 256. 2167 of 2231 steps (97%) done [Fri Nov 3 10:51:40 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1998.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1998.PRE.gff, analyses/output/Amil-MirMachine/Mir-1998.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1998.PRE.unfiltered jobid: 255 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1998.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1998.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1998.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:40 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-276.PRE.CM output: analyses/output/Amil-MirMachine/Mir-276.PRE.result jobid: 436 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-276.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-276.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:40 2023] Finished job 255. 2168 of 2231 steps (97%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-1998.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:40 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1998.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1998.PRE.filtered.gff jobid: 1242 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1998.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1998.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1998.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:40 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1998.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1998.PRE.filtered.fasta jobid: 1801 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1998.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1998.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1998.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:40 2023] Finished job 1801. 2169 of 2231 steps (97%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:40 2023] Finished job 1242. 2170 of 2231 steps (97%) done [Fri Nov 3 10:51:42 2023] Finished job 556. 2171 of 2231 steps (97%) done [Fri Nov 3 10:51:42 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-357.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-357.PRE.gff, analyses/output/Amil-MirMachine/Mir-357.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-357.PRE.unfiltered jobid: 555 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-357.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-357.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-357.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:42 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-4861.PRE.CM output: analyses/output/Amil-MirMachine/Mir-4861.PRE.result jobid: 676 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4861.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4861.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:42 2023] Finished job 555. 2172 of 2231 steps (97%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-357.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:42 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-357.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-357.PRE.filtered.fasta jobid: 1951 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-357.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-357.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-357.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:42 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-357.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-357.PRE.filtered.gff jobid: 1392 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-357.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-357.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-357.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:42 2023] Finished job 1951. 2173 of 2231 steps (97%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:42 2023] Finished job 1392. 2174 of 2231 steps (97%) done [Fri Nov 3 10:51:45 2023] Finished job 436. 2175 of 2231 steps (97%) done [Fri Nov 3 10:51:45 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-992.PRE.CM output: analyses/output/Amil-MirMachine/Mir-992.PRE.result jobid: 1110 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-992.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-992.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:45 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-276.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-276.PRE.gff, analyses/output/Amil-MirMachine/Mir-276.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-276.PRE.unfiltered jobid: 435 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-276.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-276.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-276.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:45 2023] Finished job 435. 2176 of 2231 steps (98%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-276.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:45 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-276.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-276.PRE.filtered.fasta jobid: 1891 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-276.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-276.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-276.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:45 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-276.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-276.PRE.filtered.gff jobid: 1332 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-276.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-276.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-276.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:45 2023] Finished job 1891. 2177 of 2231 steps (98%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:45 2023] Finished job 1332. 2178 of 2231 steps (98%) done [Fri Nov 3 10:51:46 2023] Finished job 676. 2179 of 2231 steps (98%) done [Fri Nov 3 10:51:46 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-392.PRE.CM output: analyses/output/Amil-MirMachine/Mir-392.PRE.result jobid: 584 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-392.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-392.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:46 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-4861.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-4861.PRE.gff, analyses/output/Amil-MirMachine/Mir-4861.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-4861.PRE.unfiltered jobid: 675 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4861.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-4861.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-4861.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:46 2023] Finished job 675. 2180 of 2231 steps (98%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-4861.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:46 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-4861.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4861.PRE.filtered.fasta jobid: 2011 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4861.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4861.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4861.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:46 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-4861.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-4861.PRE.filtered.gff jobid: 1452 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-4861.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-4861.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-4861.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:46 2023] Finished job 2011. 2181 of 2231 steps (98%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:46 2023] Finished job 1452. 2182 of 2231 steps (98%) done [Fri Nov 3 10:51:58 2023] Finished job 1110. 2183 of 2231 steps (98%) done [Fri Nov 3 10:51:58 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-992.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-992.PRE.gff, analyses/output/Amil-MirMachine/Mir-992.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-992.PRE.unfiltered jobid: 1109 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-992.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-992.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-992.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:58 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-70.PRE.CM output: analyses/output/Amil-MirMachine/Mir-70.PRE.result jobid: 826 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-70.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-70.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:51:58 2023] Finished job 1109. 2184 of 2231 steps (98%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-992.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:51:58 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-992.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-992.PRE.filtered.gff jobid: 1669 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-992.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-992.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-992.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:58 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-992.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-992.PRE.filtered.fasta jobid: 2228 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-992.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-992.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-992.PRE resources: tmpdir=/tmp [Fri Nov 3 10:51:58 2023] Finished job 2228. 2185 of 2231 steps (98%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:51:58 2023] Finished job 1669. 2186 of 2231 steps (98%) done [Fri Nov 3 10:52:06 2023] Finished job 584. 2187 of 2231 steps (98%) done [Fri Nov 3 10:52:06 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-652.PRE.CM output: analyses/output/Amil-MirMachine/Mir-652.PRE.result jobid: 796 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-652.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-652.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:52:06 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-392.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-392.PRE.gff, analyses/output/Amil-MirMachine/Mir-392.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-392.PRE.unfiltered jobid: 583 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-392.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-392.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-392.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:06 2023] Finished job 583. 2188 of 2231 steps (98%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-392.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:06 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-392.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-392.PRE.filtered.gff jobid: 1406 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-392.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-392.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-392.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:06 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-392.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-392.PRE.filtered.fasta jobid: 1965 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-392.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-392.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-392.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:06 2023] Finished job 1965. 2189 of 2231 steps (98%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:06 2023] Finished job 1406. 2190 of 2231 steps (98%) done [Fri Nov 3 10:52:09 2023] Finished job 796. 2191 of 2231 steps (98%) done [Fri Nov 3 10:52:09 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-652.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-652.PRE.gff, analyses/output/Amil-MirMachine/Mir-652.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-652.PRE.unfiltered jobid: 795 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-652.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-652.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-652.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:09 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-314.PRE.CM output: analyses/output/Amil-MirMachine/Mir-314.PRE.result jobid: 496 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-314.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-314.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:52:09 2023] Finished job 795. 2192 of 2231 steps (98%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-652.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-652.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-652.PRE.filtered.fasta jobid: 2071 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-652.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-652.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-652.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-652.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-652.PRE.filtered.gff jobid: 1512 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-652.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-652.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-652.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:10 2023] Finished job 2071. 2193 of 2231 steps (98%) done Select jobs to execute... [Fri Nov 3 10:52:10 2023] Finished job 826. 2194 of 2231 steps (98%) done [Fri Nov 3 10:52:10 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-70.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-70.PRE.gff, analyses/output/Amil-MirMachine/Mir-70.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-70.PRE.unfiltered jobid: 825 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-70.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-70.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-70.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:10 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-651.PRE.CM output: analyses/output/Amil-MirMachine/Mir-651.PRE.result jobid: 794 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-651.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-651.PRE threads: 15 resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:52:10 2023] Finished job 825. 2195 of 2231 steps (98%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-70.PRE.ext.gff. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:10 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-70.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-70.PRE.filtered.gff jobid: 1527 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-70.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-70.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-70.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:10 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-70.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-70.PRE.filtered.fasta jobid: 2086 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-70.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-70.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-70.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:10 2023] Finished job 1512. 2196 of 2231 steps (98%) done Select jobs to execute... [Fri Nov 3 10:52:10 2023] Finished job 2086. 2197 of 2231 steps (98%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:10 2023] Finished job 1527. 2198 of 2231 steps (99%) done [Fri Nov 3 10:52:18 2023] Finished job 496. 2199 of 2231 steps (99%) done [Fri Nov 3 10:52:18 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-3112.PRE.CM output: analyses/output/Amil-MirMachine/Mir-3112.PRE.result jobid: 494 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3112.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-3112.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:52:18 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-314.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-314.PRE.gff, analyses/output/Amil-MirMachine/Mir-314.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-314.PRE.unfiltered jobid: 495 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-314.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-314.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-314.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:18 2023] Finished job 495. 2200 of 2231 steps (99%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-314.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:18 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-314.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-314.PRE.filtered.gff jobid: 1362 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-314.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-314.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-314.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:18 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-314.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-314.PRE.filtered.fasta jobid: 1921 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-314.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-314.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-314.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:18 2023] Finished job 1921. 2201 of 2231 steps (99%) done Select jobs to execute... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:18 2023] Finished job 1362. 2202 of 2231 steps (99%) done [Fri Nov 3 10:52:27 2023] Finished job 794. 2203 of 2231 steps (99%) done [Fri Nov 3 10:52:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-651.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-651.PRE.gff, analyses/output/Amil-MirMachine/Mir-651.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-651.PRE.unfiltered jobid: 793 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-651.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-651.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-651.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-355.PRE.CM output: analyses/output/Amil-MirMachine/Mir-355.PRE.result jobid: 554 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-355.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-355.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:52:27 2023] Finished job 793. 2204 of 2231 steps (99%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-651.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-651.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-651.PRE.filtered.gff jobid: 1511 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-651.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-651.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-651.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-651.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-651.PRE.filtered.fasta jobid: 2070 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-651.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-651.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-651.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:27 2023] Finished job 2070. 2205 of 2231 steps (99%) done Select jobs to execute... [Fri Nov 3 10:52:27 2023] Finished job 494. 2206 of 2231 steps (99%) done [Fri Nov 3 10:52:27 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-328.PRE.CM output: analyses/output/Amil-MirMachine/Mir-328.PRE.result jobid: 524 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-328.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-328.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:52:27 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-3112.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-3112.PRE.gff, analyses/output/Amil-MirMachine/Mir-3112.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-3112.PRE.unfiltered jobid: 493 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3112.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3112.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-3112.PRE resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:52:27 2023] Finished job 493. 2207 of 2231 steps (99%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-3112.PRE.ext.gff. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:27 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-3112.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3112.PRE.filtered.gff jobid: 1361 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3112.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3112.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3112.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:27 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-3112.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-3112.PRE.filtered.fasta jobid: 1920 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-3112.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-3112.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-3112.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:27 2023] Finished job 1920. 2208 of 2231 steps (99%) done Select jobs to execute... [Fri Nov 3 10:52:27 2023] Finished job 1511. 2209 of 2231 steps (99%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:27 2023] Finished job 1361. 2210 of 2231 steps (99%) done [Fri Nov 3 10:52:32 2023] Finished job 524. 2211 of 2231 steps (99%) done [Fri Nov 3 10:52:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-760.PRE.CM output: analyses/output/Amil-MirMachine/Mir-760.PRE.result jobid: 944 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-760.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-760.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:52:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-328.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-328.PRE.gff, analyses/output/Amil-MirMachine/Mir-328.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-328.PRE.unfiltered jobid: 523 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-328.PRE.gff; Input files updated by another job: data/genomes/Amil-MirMachine.size, analyses/output/Amil-MirMachine/Mir-328.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-328.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:32 2023] Finished job 523. 2212 of 2231 steps (99%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-328.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:32 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-328.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-328.PRE.filtered.gff jobid: 1376 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-328.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-328.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-328.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:32 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-328.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-328.PRE.filtered.fasta jobid: 1935 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-328.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-328.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-328.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:32 2023] Finished job 554. 2213 of 2231 steps (99%) done Select jobs to execute... [Fri Nov 3 10:52:32 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-355.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-355.PRE.gff, analyses/output/Amil-MirMachine/Mir-355.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-355.PRE.unfiltered jobid: 553 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-355.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-355.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:32 2023] rule search_CM: input: /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cms/combined/Mir-1997.PRE.CM output: analyses/output/Amil-MirMachine/Mir-1997.PRE.result jobid: 254 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1997.PRE.result wildcards: species=Amil-MirMachine, mirna=Mir-1997.PRE threads: 15 resources: tmpdir=/tmp [Fri Nov 3 10:52:32 2023] Finished job 1935. 2214 of 2231 steps (99%) done [Fri Nov 3 10:52:33 2023] Finished job 553. 2215 of 2231 steps (99%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-355.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:33 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-355.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-355.PRE.filtered.gff jobid: 1391 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-355.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-355.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:33 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-355.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-355.PRE.filtered.fasta jobid: 1950 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-355.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-355.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-355.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:33 2023] Finished job 1950. 2216 of 2231 steps (99%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:33 2023] Finished job 1376. 2217 of 2231 steps (99%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:33 2023] Finished job 1391. 2218 of 2231 steps (99%) done [Fri Nov 3 10:52:36 2023] Finished job 944. 2219 of 2231 steps (99%) done Select jobs to execute... [Fri Nov 3 10:52:36 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-760.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-760.PRE.gff, analyses/output/Amil-MirMachine/Mir-760.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-760.PRE.unfiltered jobid: 943 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-760.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-760.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-760.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:36 2023] Finished job 943. 2220 of 2231 steps (99.5%) done Removing temporary output analyses/output/Amil-MirMachine/Mir-760.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:36 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-760.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-760.PRE.filtered.gff jobid: 1586 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-760.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-760.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-760.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:36 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-760.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-760.PRE.filtered.fasta jobid: 2145 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-760.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-760.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-760.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:36 2023] Finished job 2145. 2221 of 2231 steps (99.6%) done Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:36 2023] Finished job 1586. 2222 of 2231 steps (99.6%) done [Fri Nov 3 10:52:38 2023] Finished job 254. 2223 of 2231 steps (99.6%) done Select jobs to execute... [Fri Nov 3 10:52:38 2023] rule parse_output: input: analyses/output/Amil-MirMachine/Mir-1997.PRE.result, data/genomes/Amil-MirMachine.size output: analyses/output/Amil-MirMachine/Mir-1997.PRE.gff, analyses/output/Amil-MirMachine/Mir-1997.PRE.ext.gff, analyses/output/Amil-MirMachine/Mir-1997.PRE.unfiltered jobid: 253 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1997.PRE.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1997.PRE.result, data/genomes/Amil-MirMachine.size wildcards: species=Amil-MirMachine, mirna=Mir-1997.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:38 2023] Finished job 253. 2224 of 2231 steps (99.7%) done Removing temporary output data/genomes/Amil-MirMachine.size. Removing temporary output analyses/output/Amil-MirMachine/Mir-1997.PRE.ext.gff. Select jobs to execute... [Fri Nov 3 10:52:38 2023] rule create_filtered_gffs: input: analyses/output/Amil-MirMachine/Mir-1997.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1997.PRE.filtered.gff jobid: 1241 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1997.PRE.filtered.gff; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1997.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1997.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:38 2023] rule combine_gffs: input: analyses/output/Amil-MirMachine/Bantam.PRE.gff, analyses/output/Amil-MirMachine/Iab-4.PRE.gff, analyses/output/Amil-MirMachine/Let-7.PRE.gff, analyses/output/Amil-MirMachine/Lsy-6.PRE.gff, analyses/output/Amil-MirMachine/Mir-1.PRE.gff, analyses/output/Amil-MirMachine/Mir-10.PRE.gff, analyses/output/Amil-MirMachine/Mir-1000.PRE.gff, analyses/output/Amil-MirMachine/Mir-1001.PRE.gff, analyses/output/Amil-MirMachine/Mir-1003.PRE.gff, analyses/output/Amil-MirMachine/Mir-1006.PRE.gff, analyses/output/Amil-MirMachine/Mir-1007.PRE.gff, analyses/output/Amil-MirMachine/Mir-101.PRE.gff, analyses/output/Amil-MirMachine/Mir-1010.PRE.gff, analyses/output/Amil-MirMachine/Mir-103.PRE.gff, analyses/output/Amil-MirMachine/Mir-105.PRE.gff, analyses/output/Amil-MirMachine/Mir-1175.PRE.gff, analyses/output/Amil-MirMachine/Mir-1180.PRE.gff, analyses/output/Amil-MirMachine/Mir-12.PRE.gff, analyses/output/Amil-MirMachine/Mir-12085.PRE.gff, analyses/output/Amil-MirMachine/Mir-12086.PRE.gff, analyses/output/Amil-MirMachine/Mir-12087.PRE.gff, analyses/output/Amil-MirMachine/Mir-122.PRE.gff, analyses/output/Amil-MirMachine/Mir-12316.PRE.gff, analyses/output/Amil-MirMachine/Mir-12355.PRE.gff, analyses/output/Amil-MirMachine/Mir-12358.PRE.gff, analyses/output/Amil-MirMachine/Mir-12366.PRE.gff, analyses/output/Amil-MirMachine/Mir-12380.PRE.gff, analyses/output/Amil-MirMachine/Mir-124.PRE.gff, analyses/output/Amil-MirMachine/Mir-12404.PRE.gff, analyses/output/Amil-MirMachine/Mir-1247.PRE.gff, analyses/output/Amil-MirMachine/Mir-1249.PRE.gff, analyses/output/Amil-MirMachine/Mir-1251.PRE.gff, analyses/output/Amil-MirMachine/Mir-126.PRE.gff, analyses/output/Amil-MirMachine/Mir-127.PRE.gff, analyses/output/Amil-MirMachine/Mir-1271.PRE.gff, analyses/output/Amil-MirMachine/Mir-1277.PRE.gff, analyses/output/Amil-MirMachine/Mir-128.PRE.gff, analyses/output/Amil-MirMachine/Mir-129.PRE.gff, analyses/output/Amil-MirMachine/Mir-1296.PRE.gff, analyses/output/Amil-MirMachine/Mir-1298.PRE.gff, analyses/output/Amil-MirMachine/Mir-130.PRE.gff, analyses/output/Amil-MirMachine/Mir-1301.PRE.gff, analyses/output/Amil-MirMachine/Mir-1306.PRE.gff, analyses/output/Amil-MirMachine/Mir-1307.PRE.gff, analyses/output/Amil-MirMachine/Mir-132.PRE.gff, analyses/output/Amil-MirMachine/Mir-1323.PRE.gff, analyses/output/Amil-MirMachine/Mir-1329.PRE.gff, analyses/output/Amil-MirMachine/Mir-133.PRE.gff, analyses/output/Amil-MirMachine/Mir-134.PRE.gff, analyses/output/Amil-MirMachine/Mir-1343.PRE.gff, analyses/output/Amil-MirMachine/Mir-135.PRE.gff, analyses/output/Amil-MirMachine/Mir-136.PRE.gff, analyses/output/Amil-MirMachine/Mir-137.PRE.gff, analyses/output/Amil-MirMachine/Mir-1379.PRE.gff, analyses/output/Amil-MirMachine/Mir-138.PRE.gff, analyses/output/Amil-MirMachine/Mir-1388.PRE.gff, analyses/output/Amil-MirMachine/Mir-139.PRE.gff, analyses/output/Amil-MirMachine/Mir-1397.PRE.gff, analyses/output/Amil-MirMachine/Mir-14.PRE.gff, analyses/output/Amil-MirMachine/Mir-140.PRE.gff, analyses/output/Amil-MirMachine/Mir-1416.PRE.gff, analyses/output/Amil-MirMachine/Mir-142.PRE.gff, analyses/output/Amil-MirMachine/Mir-143.PRE.gff, analyses/output/Amil-MirMachine/Mir-144.PRE.gff, analyses/output/Amil-MirMachine/Mir-145.PRE.gff, analyses/output/Amil-MirMachine/Mir-1451.PRE.gff, analyses/output/Amil-MirMachine/Mir-146.PRE.gff, analyses/output/Amil-MirMachine/Mir-1467.PRE.gff, analyses/output/Amil-MirMachine/Mir-147.PRE.gff, analyses/output/Amil-MirMachine/Mir-148.PRE.gff, analyses/output/Amil-MirMachine/Mir-149.PRE.gff, analyses/output/Amil-MirMachine/Mir-15.PRE.gff, analyses/output/Amil-MirMachine/Mir-150.PRE.gff, analyses/output/Amil-MirMachine/Mir-153.PRE.gff, analyses/output/Amil-MirMachine/Mir-154.PRE.gff, analyses/output/Amil-MirMachine/Mir-1540.PRE.gff, analyses/output/Amil-MirMachine/Mir-1541.PRE.gff, analyses/output/Amil-MirMachine/Mir-1542.PRE.gff, analyses/output/Amil-MirMachine/Mir-1546.PRE.gff, analyses/output/Amil-MirMachine/Mir-1547.PRE.gff, analyses/output/Amil-MirMachine/Mir-1549.PRE.gff, analyses/output/Amil-MirMachine/Mir-155.PRE.gff, analyses/output/Amil-MirMachine/Mir-1552.PRE.gff, analyses/output/Amil-MirMachine/Mir-1559.PRE.gff, analyses/output/Amil-MirMachine/Mir-1641.PRE.gff, analyses/output/Amil-MirMachine/Mir-1662.PRE.gff, analyses/output/Amil-MirMachine/Mir-1677.PRE.gff, analyses/output/Amil-MirMachine/Mir-17.PRE.gff, analyses/output/Amil-MirMachine/Mir-1720.PRE.gff, analyses/output/Amil-MirMachine/Mir-1729.PRE.gff, analyses/output/Amil-MirMachine/Mir-1781.PRE.gff, analyses/output/Amil-MirMachine/Mir-1788.PRE.gff, analyses/output/Amil-MirMachine/Mir-1805.PRE.gff, analyses/output/Amil-MirMachine/Mir-181.PRE.gff, analyses/output/Amil-MirMachine/Mir-1817.PRE.gff, analyses/output/Amil-MirMachine/Mir-184.PRE.gff, analyses/output/Amil-MirMachine/Mir-1842.PRE.gff, analyses/output/Amil-MirMachine/Mir-185.PRE.gff, analyses/output/Amil-MirMachine/Mir-186.PRE.gff, analyses/output/Amil-MirMachine/Mir-187.PRE.gff, analyses/output/Amil-MirMachine/Mir-188.PRE.gff, analyses/output/Amil-MirMachine/Mir-19.PRE.gff, analyses/output/Amil-MirMachine/Mir-190.PRE.gff, analyses/output/Amil-MirMachine/Mir-191.PRE.gff, analyses/output/Amil-MirMachine/Mir-1911.PRE.gff, analyses/output/Amil-MirMachine/Mir-1912.PRE.gff, analyses/output/Amil-MirMachine/Mir-192.PRE.gff, analyses/output/Amil-MirMachine/Mir-193.PRE.gff, analyses/output/Amil-MirMachine/Mir-194.PRE.gff, analyses/output/Amil-MirMachine/Mir-1955.PRE.gff, analyses/output/Amil-MirMachine/Mir-196.PRE.gff, analyses/output/Amil-MirMachine/Mir-1962.PRE.gff, analyses/output/Amil-MirMachine/Mir-197.PRE.gff, analyses/output/Amil-MirMachine/Mir-1984.PRE.gff, analyses/output/Amil-MirMachine/Mir-1985.PRE.gff, analyses/output/Amil-MirMachine/Mir-1986.PRE.gff, analyses/output/Amil-MirMachine/Mir-1987.PRE.gff, analyses/output/Amil-MirMachine/Mir-1989.PRE.gff, analyses/output/Amil-MirMachine/Mir-199.PRE.gff, analyses/output/Amil-MirMachine/Mir-1990.PRE.gff, analyses/output/Amil-MirMachine/Mir-1992.PRE.gff, analyses/output/Amil-MirMachine/Mir-1993.PRE.gff, analyses/output/Amil-MirMachine/Mir-1994.PRE.gff, analyses/output/Amil-MirMachine/Mir-1995.PRE.gff, analyses/output/Amil-MirMachine/Mir-1996.PRE.gff, analyses/output/Amil-MirMachine/Mir-1997.PRE.gff, analyses/output/Amil-MirMachine/Mir-1998.PRE.gff, analyses/output/Amil-MirMachine/Mir-2.PRE.gff, analyses/output/Amil-MirMachine/Mir-2000.PRE.gff, analyses/output/Amil-MirMachine/Mir-2001.PRE.gff, analyses/output/Amil-MirMachine/Mir-2002.PRE.gff, analyses/output/Amil-MirMachine/Mir-2004.PRE.gff, analyses/output/Amil-MirMachine/Mir-2005.PRE.gff, analyses/output/Amil-MirMachine/Mir-2006.PRE.gff, analyses/output/Amil-MirMachine/Mir-2007.PRE.gff, analyses/output/Amil-MirMachine/Mir-2008.PRE.gff, analyses/output/Amil-MirMachine/Mir-2009.PRE.gff, analyses/output/Amil-MirMachine/Mir-2010.PRE.gff, analyses/output/Amil-MirMachine/Mir-2011.PRE.gff, analyses/output/Amil-MirMachine/Mir-2012.PRE.gff, analyses/output/Amil-MirMachine/Mir-2014.PRE.gff, analyses/output/Amil-MirMachine/Mir-2015.PRE.gff, analyses/output/Amil-MirMachine/Mir-2017.PRE.gff, analyses/output/Amil-MirMachine/Mir-2018.PRE.gff, analyses/output/Amil-MirMachine/Mir-2019.PRE.gff, analyses/output/Amil-MirMachine/Mir-202.PRE.gff, 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analyses/output/Amil-MirMachine/Mir-8160.PRE.gff, analyses/output/Amil-MirMachine/Mir-135.PRE.gff, analyses/output/Amil-MirMachine/Mir-511.PRE.gff, analyses/output/Amil-MirMachine/Mir-7378.PRE.gff, analyses/output/Amil-MirMachine/Mir-969.PRE.gff, analyses/output/Amil-MirMachine/Mir-217.PRE.gff, analyses/output/Amil-MirMachine/Mir-460.PRE.gff, analyses/output/Amil-MirMachine/Mir-137.PRE.gff, analyses/output/Amil-MirMachine/Mir-452.PRE.gff, analyses/output/Amil-MirMachine/Mir-2007.PRE.gff wildcards: species=Amil-MirMachine resources: tmpdir=/tmp [Fri Nov 3 10:52:38 2023] rule fastas: input: analyses/output/Amil-MirMachine/Mir-1997.PRE.gff, /home/sam/programs/mambaforge/envs/mirmachine_env/lib/python3.10/site-packages/mirmachine/meta/cutoffs/combined/mirmachine_trusted_cutoffs.tsv output: analyses/output/Amil-MirMachine/Mir-1997.PRE.filtered.fasta jobid: 1800 reason: Missing output files: analyses/output/Amil-MirMachine/Mir-1997.PRE.filtered.fasta; Input files updated by another job: analyses/output/Amil-MirMachine/Mir-1997.PRE.gff wildcards: species=Amil-MirMachine, mirna=Mir-1997.PRE resources: tmpdir=/tmp [Fri Nov 3 10:52:38 2023] Finished job 1800. 2225 of 2231 steps (99.7%) done Select jobs to execute... [Fri Nov 3 10:52:38 2023] rule combine_fastas: input: analyses/output/Amil-MirMachine/Bantam.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Iab-4.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Let-7.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Lsy-6.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-10.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1000.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1001.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1003.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1006.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1007.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-101.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1010.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-103.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-105.PRE.filtered.fasta, 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analyses/output/Amil-MirMachine/Mir-2191.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-126.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-4057.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-1298.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-7147.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-2689.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-3075.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-335.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-190.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-4835.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-769.PRE.filtered.fasta, analyses/output/Amil-MirMachine/Mir-204.PRE.filtered.fasta wildcards: species=Amil-MirMachine resources: tmpdir=/tmp Building DAG of jobs... Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... Building DAG of jobs... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:38 2023] Finished job 1241. 2226 of 2231 steps (99.8%) done Select jobs to execute... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... [Fri Nov 3 10:52:38 2023] rule combine_filtered_gffs: input: analyses/output/Amil-MirMachine/Bantam.PRE.filtered.gff, analyses/output/Amil-MirMachine/Iab-4.PRE.filtered.gff, analyses/output/Amil-MirMachine/Let-7.PRE.filtered.gff, analyses/output/Amil-MirMachine/Lsy-6.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-10.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1000.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1001.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1003.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1006.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1007.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-101.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1010.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-103.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-105.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1175.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1180.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12085.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12086.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12087.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-122.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12316.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12355.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12358.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12366.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12380.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-124.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-12404.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1247.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1249.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1251.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-126.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-127.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1271.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1277.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-128.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-129.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1296.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1298.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-130.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1301.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1306.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1307.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-132.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1323.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1329.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-133.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-134.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1343.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-135.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-136.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-137.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1379.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-138.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1388.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-139.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1397.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-14.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-140.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1416.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-142.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-143.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-144.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-145.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1451.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-146.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1467.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-147.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-148.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-149.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-15.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-150.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-153.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-154.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1540.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1541.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1542.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1546.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1547.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1549.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-155.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1552.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1559.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1641.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1662.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1677.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-17.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1720.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1729.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1781.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1788.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1805.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-181.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1817.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-184.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1842.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-185.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-186.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-187.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-188.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-19.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-190.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-191.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1911.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1912.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-192.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-193.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-194.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1955.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-196.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1962.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-197.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1984.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1985.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1986.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1987.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1989.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-199.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1990.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1992.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1993.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1994.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1995.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1996.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1997.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1998.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2000.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2001.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2002.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2004.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2005.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2006.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2007.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2008.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2009.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2010.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2011.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2012.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2014.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2015.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2017.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2018.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2019.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-202.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2020.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2021.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2022.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-203.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2030.PRE.filtered.gff, 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analyses/output/Amil-MirMachine/Mir-2004.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-355.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-1805.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-4859.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-642.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-23.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-276.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2691.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-132.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-73.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-6529.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-2008.PRE.filtered.gff, analyses/output/Amil-MirMachine/Mir-964.PRE.filtered.gff wildcards: species=Amil-MirMachine resources: tmpdir=/tmp Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:39 2023] Finished job 1. 2227 of 2231 steps (99.8%) done [Fri Nov 3 10:52:39 2023] Finished job 1674. 2228 of 2231 steps (99.9%) done Removing temporary output analyses/output/Amil-MirMachine/Bantam.PRE.filtered.fasta. 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Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:39 2023] Finished job 1115. 2229 of 2231 steps (99.9%) done Removing temporary output analyses/output/Amil-MirMachine/Bantam.PRE.filtered.gff. 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[Fri Nov 3 10:52:39 2023] rule create_heatmap_csv: input: results/predictions/gff/Amil-MirMachine.PRE.gff, results/predictions/filtered_gff/Amil-MirMachine.PRE.gff, analyses/search/Amil-MirMachine.mirna_nodes.csv output: results/predictions/gff/Amil-MirMachine.csv, results/predictions/filtered_gff/Amil-MirMachine.csv, results/predictions/heatmap/Amil-MirMachine.csv, results/predictions/heatmap/Amil-MirMachine.heatmap.csv jobid: 1672 reason: Missing output files: results/predictions/heatmap/Amil-MirMachine.heatmap.csv; Input files updated by another job: results/predictions/gff/Amil-MirMachine.PRE.gff, analyses/search/Amil-MirMachine.mirna_nodes.csv, results/predictions/filtered_gff/Amil-MirMachine.PRE.gff wildcards: species=Amil-MirMachine resources: tmpdir=/tmp Building DAG of jobs... Using shell: /bin/bash Provided cores: 40 Rules claiming more threads will be scaled down. Select jobs to execute... ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] [Fri Nov 3 10:52:39 2023] Finished job 1672. 2230 of 2231 steps (100.0%) done Removing temporary output results/predictions/gff/Amil-MirMachine.csv. Removing temporary output results/predictions/filtered_gff/Amil-MirMachine.csv. Removing temporary output results/predictions/heatmap/Amil-MirMachine.csv. Select jobs to execute... [Fri Nov 3 10:52:39 2023] localrule all: input: results/predictions/gff/Amil-MirMachine.PRE.gff, results/predictions/filtered_gff/Amil-MirMachine.PRE.gff, results/predictions/heatmap/Amil-MirMachine.heatmap.csv, results/predictions/fasta/Amil-MirMachine.PRE.fasta jobid: 0 reason: Input files updated by another job: results/predictions/heatmap/Amil-MirMachine.heatmap.csv, results/predictions/fasta/Amil-MirMachine.PRE.fasta, results/predictions/gff/Amil-MirMachine.PRE.gff, results/predictions/filtered_gff/Amil-MirMachine.PRE.gff resources: tmpdir=/tmp [Fri Nov 3 10:52:39 2023] Finished job 0. 2231 of 2231 steps (100%) done Complete log: .snakemake/log/2023-11-03T102116.239209.snakemake.log ##gff-version 3 # MirMachine version: 0.2.12 # CM Models: Built using MirGeneDB 2.1(2022) # Total families searched: 556 # Node: Metazoa # Model: combined # Genome file: /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna # Species: Amil-MirMachine # Params: /home/sam/programs/mambaforge/envs/mirmachine_env/bin/MirMachine.py --node Metazoa --species Amil-MirMachine --genome /home/shared/8TB_HDD_01/sam/gitrepos/deep-dive/D-Apul/data/Amil/ncbi_dataset/data/GCF_013753865.1/GCF_013753865.1_Amil_v2.1_genomic.fna --cpu 40 --add-all-nodes # miRNAs families searched: ['BANTAM', 'IAB-4', 'LET-7', 'LSY-6', 'MIR-1', 'MIR-10', 'MIR-1000', 'MIR-1001', 'MIR-1003', 'MIR-1006', 'MIR-1007', 'MIR-101', 'MIR-1010', 'MIR-103', 'MIR-105', 'MIR-1175', 'MIR-1180', 'MIR-12', 'MIR-12085', 'MIR-12086', 'MIR-12087', 'MIR-122', 'MIR-12316', 'MIR-12355', 'MIR-12358', 'MIR-12366', 'MIR-12380', 'MIR-124', 'MIR-12404', 'MIR-1247', 'MIR-1249', 'MIR-1251', 'MIR-126', 'MIR-127', 'MIR-1271', 'MIR-1277', 'MIR-128', 'MIR-129', 'MIR-1296', 'MIR-1298', 'MIR-130', 'MIR-1301', 'MIR-1306', 'MIR-1307', 'MIR-132', 'MIR-1323', 'MIR-1329', 'MIR-133', 'MIR-134', 'MIR-1343', 'MIR-135', 'MIR-136', 'MIR-137', 'MIR-1379', 'MIR-138', 'MIR-1388', 'MIR-139', 'MIR-1397', 'MIR-14', 'MIR-140', 'MIR-1416', 'MIR-142', 'MIR-143', 'MIR-144', 'MIR-145', 'MIR-1451', 'MIR-146', 'MIR-1467', 'MIR-147', 'MIR-148', 'MIR-149', 'MIR-15', 'MIR-150', 'MIR-153', 'MIR-154', 'MIR-1540', 'MIR-1541', 'MIR-1542', 'MIR-1546', 'MIR-1547', 'MIR-1549', 'MIR-155', 'MIR-1552', 'MIR-1559', 'MIR-1641', 'MIR-1662', 'MIR-1677', 'MIR-17', 'MIR-1720', 'MIR-1729', 'MIR-1781', 'MIR-1788', 'MIR-1805', 'MIR-181', 'MIR-1817', 'MIR-184', 'MIR-1842', 'MIR-185', 'MIR-186', 'MIR-187', 'MIR-188', 'MIR-19', 'MIR-190', 'MIR-191', 'MIR-1911', 'MIR-1912', 'MIR-192', 'MIR-193', 'MIR-194', 'MIR-1955', 'MIR-196', 'MIR-1962', 'MIR-197', 'MIR-1984', 'MIR-1985', 'MIR-1986', 'MIR-1987', 'MIR-1989', 'MIR-199', 'MIR-1990', 'MIR-1992', 'MIR-1993', 'MIR-1994', 'MIR-1995', 'MIR-1996', 'MIR-1997', 'MIR-1998', 'MIR-2', 'MIR-2000', 'MIR-2001', 'MIR-2002', 'MIR-2004', 'MIR-2005', 'MIR-2006', 'MIR-2007', 'MIR-2008', 'MIR-2009', 'MIR-2010', 'MIR-2011', 'MIR-2012', 'MIR-2014', 'MIR-2015', 'MIR-2017', 'MIR-2018', 'MIR-2019', 'MIR-202', 'MIR-2020', 'MIR-2021', 'MIR-2022', 'MIR-203', 'MIR-2030', 'MIR-204', 'MIR-205', 'MIR-2056', 'MIR-2057', 'MIR-2058', 'MIR-2061', 'MIR-2062', 'MIR-2068', 'MIR-2070', 'MIR-2071', 'MIR-2072', 'MIR-2076', 'MIR-208', 'MIR-21', 'MIR-210', 'MIR-2114', 'MIR-2131', 'MIR-214', 'MIR-216', 'MIR-217', 'MIR-218', 'MIR-2184', 'MIR-2188', 'MIR-2189', 'MIR-219', 'MIR-2191', 'MIR-22', 'MIR-221', 'MIR-223', 'MIR-224', 'MIR-2279', 'MIR-23', 'MIR-230', 'MIR-231', 'MIR-2355', 'MIR-238', 'MIR-2387', 'MIR-24', 'MIR-242', 'MIR-246', 'MIR-248', 'MIR-2483', 'MIR-249', 'MIR-2499', 'MIR-2501', 'MIR-252', 'MIR-253', 'MIR-254', 'MIR-255', 'MIR-2582', 'MIR-2583', 'MIR-2584', 'MIR-26', 'MIR-2685', 'MIR-2686', 'MIR-2687', 'MIR-2689', 'MIR-2690', 'MIR-2691', 'MIR-2693', 'MIR-27', 'MIR-2705', 'MIR-2707', 'MIR-2722', 'MIR-275', 'MIR-276', 'MIR-2765', 'MIR-277', 'MIR-278', 'MIR-279', 'MIR-2796', 'MIR-28', 'MIR-281', 'MIR-282', 'MIR-284', 'MIR-29', 'MIR-2954', 'MIR-296', 'MIR-2970', 'MIR-298', 'MIR-2984', 'MIR-3', 'MIR-30', 'MIR-303', 'MIR-3049', 'MIR-305', 'MIR-3059', 'MIR-306', 'MIR-3068', 'MIR-3072', 'MIR-3075', 'MIR-3085', 'MIR-3099', 'MIR-31', 'MIR-3112', 'MIR-314', 'MIR-3140', 'MIR-3145', 'MIR-3146', 'MIR-315', 'MIR-316', 'MIR-317', 'MIR-3173', 'MIR-32', 'MIR-320', 'MIR-3200', 'MIR-324', 'MIR-325', 'MIR-326', 'MIR-328', 'MIR-33', 'MIR-330', 'MIR-331', 'MIR-335', 'MIR-337', 'MIR-338', 'MIR-339', 'MIR-34', 'MIR-340', 'MIR-342', 'MIR-345', 'MIR-346', 'MIR-350', 'MIR-351', 'MIR-355', 'MIR-357', 'MIR-358', 'MIR-36', 'MIR-361', 'MIR-3613', 'MIR-3617', 'MIR-362', 'MIR-370', 'MIR-374', 'MIR-375', 'MIR-376', 'MIR-378', 'MIR-383', 'MIR-384', 'MIR-392', 'MIR-3931', 'MIR-3934', 'MIR-4057', 'MIR-423', 'MIR-425', 'MIR-430', 'MIR-431', 'MIR-432', 'MIR-433', 'MIR-448', 'MIR-450', 'MIR-451', 'MIR-452', 'MIR-4524', 'MIR-4541', 'MIR-4542', 'MIR-4543', 'MIR-4544', 'MIR-4545', 'MIR-455', 'MIR-456', 'MIR-458', 'MIR-459', 'MIR-460', 'MIR-4677', 'MIR-4766', 'MIR-4813', 'MIR-4818', 'MIR-4819', 'MIR-4820', 'MIR-4824', 'MIR-4825', 'MIR-4826', 'MIR-4828', 'MIR-4829', 'MIR-483', 'MIR-4830', 'MIR-4831', 'MIR-4835', 'MIR-4838', 'MIR-4839', 'MIR-4857', 'MIR-4859', 'MIR-486', 'MIR-4860', 'MIR-4861', 'MIR-4862', 'MIR-4863', 'MIR-4864', 'MIR-4865', 'MIR-4866', 'MIR-4869', 'MIR-4871', 'MIR-4872', 'MIR-4873', 'MIR-4874', 'MIR-4876', 'MIR-4879', 'MIR-488', 'MIR-4880', 'MIR-4886', 'MIR-4887', 'MIR-4888', 'MIR-489', 'MIR-4891', 'MIR-490', 'MIR-491', 'MIR-493', 'MIR-4969', 'MIR-498', 'MIR-4983', 'MIR-499', 'MIR-504', 'MIR-505', 'MIR-506', 'MIR-511', 'MIR-52', 'MIR-5305', 'MIR-54', 'MIR-540', 'MIR-541', 'MIR-542', 'MIR-544', 'MIR-550', 'MIR-551', 'MIR-5735', 'MIR-574', 'MIR-576', 'MIR-577', 'MIR-579', 'MIR-582', 'MIR-584', 'MIR-589', 'MIR-590', 'MIR-592', 'MIR-598', 'MIR-599', 'MIR-605', 'MIR-615', 'MIR-62', 'MIR-624', 'MIR-628', 'MIR-64', 'MIR-642', 'MIR-651', 'MIR-652', 'MIR-6529', 'MIR-653', 'MIR-666', 'MIR-667', 'MIR-67', 'MIR-670', 'MIR-671', 'MIR-6715', 'MIR-672', 'MIR-673', 'MIR-674', 'MIR-675', 'MIR-676', 'MIR-7', 'MIR-70', 'MIR-700', 'MIR-71', 'MIR-7132', 'MIR-7133', 'MIR-7147', 'MIR-7148', 'MIR-7149', 'MIR-7180', 'MIR-722', 'MIR-723', 'MIR-724', 'MIR-7246', 'MIR-7247', 'MIR-725', 'MIR-7251', 'MIR-7254', 'MIR-726', 'MIR-7262', 'MIR-727', 'MIR-728', 'MIR-7281', 'MIR-7284', 'MIR-7286', 'MIR-729', 'MIR-7292', 'MIR-7293', 'MIR-73', 'MIR-7303', 'MIR-7304', 'MIR-7309', 'MIR-7319', 'MIR-732', 'MIR-7323', 'MIR-7327', 'MIR-7332', 'MIR-7333', 'MIR-7336', 'MIR-734', 'MIR-7363', 'MIR-7368', 'MIR-737', 'MIR-7370', 'MIR-7371', 'MIR-7373', 'MIR-7376', 'MIR-7377', 'MIR-7378', 'MIR-7379', 'MIR-7383', 'MIR-7385', 'MIR-7392', 'MIR-7394', 'MIR-7397', 'MIR-7398', 'MIR-744', 'MIR-7463', 'MIR-750', 'MIR-76', 'MIR-760', 'MIR-769', 'MIR-77', 'MIR-770', 'MIR-784', 'MIR-785', 'MIR-787', 'MIR-788', 'MIR-789', 'MIR-791', 'MIR-8', 'MIR-8160', 'MIR-85', 'MIR-86', 'MIR-87', 'MIR-872', 'MIR-873', 'MIR-874', 'MIR-875', 'MIR-876', 'MIR-877', 'MIR-879', 'MIR-885', 'MIR-887', 'MIR-9', 'MIR-90', 'MIR-92', 'MIR-927', 'MIR-929', 'MIR-932', 'MIR-934', 'MIR-935', 'MIR-9369', 'MIR-9388', 'MIR-944', 'MIR-95', 'MIR-9538', 'MIR-9540', 'MIR-955', 'MIR-956', 'MIR-957', 'MIR-959', 'MIR-96', 'MIR-960', 'MIR-961', 'MIR-9619', 'MIR-962', 'MIR-963', 'MIR-964', 'MIR-965', 'MIR-966', 'MIR-967', 'MIR-9681', 'MIR-9682', 'MIR-969', 'MIR-9690', 'MIR-9692', 'MIR-9696', 'MIR-9698', 'MIR-9699', 'MIR-970', 'MIR-9701', 'MIR-9703', 'MIR-9707', 'MIR-971', 'MIR-9717', 'MIR-972', 'MIR-973', 'MIR-974', 'MIR-975', 'MIR-976', 'MIR-977', 'MIR-978', 'MIR-982', 'MIR-983', 'MIR-984', 'MIR-985', 'MIR-9851', 'MIR-986', 'MIR-987', 'MIR-988', 'MIR-989', 'MIR-991', 'MIR-992', 'MIR-997', 'MIR-999'] Total runtime: 0:31:24.712012